Digital counting of individual molecules by stochastic attachment of diverse labels

ABSTRACT

Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

RELATED APPLICATIONS

This application is a Continuation Application which claims the benefitof U.S. application Ser. No. 14/326,454 filed Jul. 8, 2014, which is aContinuation of U.S. application Ser. No. 14/281,706 filed May 19, 2014,which is a Continuation of U.S. application Ser. No. 12/969,581, nowU.S. Pat. No. 8,835,358, which claims the benefit of U.S. ProvisionalPatent Application No. 61/286,768 filed Dec. 15, 2009; U.S applicationSer. No. 14/326,454 is also a Continuation of U.S. application Ser. No.13/327,526 filed Dec. 15, 2011, which is a Continuation-in-Part of U.S.application Ser. No. 12/969,581 filed Dec. 15, 2010, now U.S. Pat. No.8,835,358; this application is also a Continuation Application whichclaims the benefit of U.S. application Ser. No. 14/326,452 filed Jul. 8,2014; which is a Continuation of U.S. application Ser. No. 14/281,706filed May 19, 2014, which is a Continuation of U.S. application Ser. No.12/969,581, now U.S. Pat. No. 8,835,358, which claims the benefit ofU.S. Provisional Patent Application No. 61/286,768 filed Dec. 15, 2009;U.S application Ser. No. 14/326,454 is also a Continuation of U.S.application Ser. No. 13/327,526 filed Dec. 15, 2011, which is aContinuation-in-Part of U.S. application Ser. No. 12/969,581 filed Dec.15, 2010, now U.S. Pat. No. 8,835,358; this application is also aContinuation Application which claims the benefit of U.S. applicationSer. No. 14/326,448 filed Jul. 8, 2014, which is a Continuation of U.S.application Ser. No. 14/281,706 filed May 19, 2014, which is aContinuation of U.S. application Ser. No. 12/969,581, now U.S. Pat. No.8,835,358, which claims the benefit of U.S. Provisional PatentApplication No. 61/286,768 filed Dec. 15, 2009; U.S application Ser. No.14/326,454 is also a Continuation of U.S. application Ser. No.13/327,526 filed Dec. 15, 2011, which is a Continuation-in-Part of U.S.application Ser. No. 12/969,581 filed Dec. 15, 2010, now U.S. Pat. No.8,835,358; this application is also a Continuation of U.S. applicationSer. No. 14/326,443 filed Jul. 8, 2014, which is a Continuation of U.S.application Ser. No. 14/281,706 filed May 19, 2014, which is aContinuation of U.S. application Ser. No. 12/969,581, now U.S. Pat. No.8,835,358, which claims the benefit of U.S. Provisional PatentApplication No. 61/286,768 filed Dec. 15, 2009; U.S application Ser. No.14/326,454 is also a Continuation of U.S. application Ser. No.13/327,526 filed Dec. 15, 2011, which is a Continuation-in-Part of U.S.application Ser. No. 12/969,581 filed Dec. 15, 2010, now U.S. Pat. No.8,835,358; this application is also a Continuation Application whichclaims the benefit of U.S. application Ser. No. 14/326,434 filed Jul. 8,2014, which is a Continuation of U.S. application Ser. No. 14/281,706filed May 19, 2014, which is a Continuation of U.S. application Ser. No.12/969,581, now U.S. Pat. No. 8,835,358, which claims the benefit ofU.S. Provisional Patent Application No. 61/286,768 filed Dec. 15, 2009;U.S application Ser. No. 14/326,454 is also a Continuation of U.S.application Ser. No. 13/327,526 filed Dec. 15, 2011, which is aContinuation-in-Part of U.S. application Ser. No. 12/969,581 filed Dec.15, 2010, now U.S. Pat. No. 8,835,358; and this application is also aContinuation Application which claims the benefit of U.S. applicationSer. No. 14/326,424 filed Jul. 8, 2014, which is a Continuation of U.S.application Ser. No. 14/281,706 filed May 19, 2014, which is aContinuation of U.S. application Ser. No. 12/969,581, now U.S. Pat. No.8,835,358, which claims the benefit of U.S. Provisional PatentApplication No. 61/286,768 filed Dec. 15, 2009; U.S application Ser. No.14/326,454 is also a Continuation of U.S. application Ser. No.13/327,526 filed Dec. 15, 2011, which is a Continuation-in-Part of U.S.application Ser. No. 12/969,581 filed Dec. 15, 2010, now U.S. Pat. No.8,835,358, the entire disclosures of which are incorporated herein byreference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Mar. 8, 2016, isnamed BDCRI-003P1C10_SEQLISTING.txt and is 392 Kilobytes in size.

FIELD OF THE INVENTION

Methods, compositions and products for counting individual molecules bystochastic attachment of diverse labels from a set of labels, followedby amplification and detection are disclosed.

BACKGROUND OF THE INVENTION

Many processes are characterized or regulated by the absolute orrelative amounts of a plurality of items. For example, in biology, thelevel of expression of particular genes or groups of genes or the numberof copies of chromosomal regions can be used to characterize the statusof a cell or tissue. Analog methods such as microarray hybridizationmethods and real-time PCR are alternatives, but digital readout methodssuch as those disclosed herein have advantages over analog methods.Methods for estimating the abundance or relative abundance of geneticmaterial having increased accuracy of counting would be beneficial.

The availability of convenient and efficient methods for the accurateidentification of genetic variation and expression patterns among largesets of genes may be applied to understanding the relationship betweenan organism's genetic make-up and the state of its health or disease,Collins et al, Science, 282: 682-689 (1998). In this regard, techniqueshave been developed for the analysis of large populations ofpolynucleotides based either on specific hybridization of probes tomicroarrays, e.g. Lockhart et al. Hacia et al, Nature Genetics, 21: 4247(1999), or on the counting of tags or signatures of DNA fragments, e.g.Velculescu et al, Science, 270: 484487 (1995); Brenner et al, NatureBiotechnology, 18: 630-634 (2000). These techniques have been used indiscovery research to identify subsets of genes that have coordinatedpatterns of expression under a variety of circumstances or that arecorrelated with, and predictive of events, of interest, such astoxicity, drug responsiveness, risk of relapse, and the like, e.g. Golubet al, Science, 286: 531-537 (1999); Alizadeh et al, Nature, 403:503-511 (2000); Perou et al, Nature, 406: 747-752 (2000); Shipp et al,Nature Medicine, 8: 68-74 (2002); Hakak et al, Proc. Natl. Acad. Sci.,98: 47454751 (2001); Thomas et al, Mol. Pharmacol., 60: 1189-1194(2001); De Primo et al, BMC Cancer 2003, 3:3; and the like. Notinfrequently the subset of genes found to be relevant has a size in therange of from ten or under to a few hundred.

In addition to gene expression, techniques have also been developed tomeasure genome-wide variation in gene copy number. For example, in thefield of oncology, there is interest in measuring genome-wide copynumber variation of local regions that characterize many cancers andthat may have diagnostic or prognostic implications. For a review seeZhang et al. Annu. Rev. Genomics Hum. Genet. 2009. 10:451-81.

While such hybridization-based techniques offer the advantages of scaleand the capability of detecting a wide range of gene expression or copynumber levels, such measurements may be subject to variability relatingto probe hybridization differences and cross-reactivity,element-to-element differences within microarrays, andmicroarray-to-microarray differences, Audic and Claverie, Genomic Res.,7: 986-995 (1997); Wittes and Friedman, J. Natl. Cancer Inst. 91:400-401 (1999).

On the other hand, techniques that provide digital representations ofabundance, such as SAGE (Velculescu et al, cited above) or MPSS (Brenneret al, cited above), are statistically more robust; they do not requirerepetition or standardization of counting experiments as countingstatistics are well-modeled by the Poisson distribution, and theprecision and accuracy of relative abundance measurements may beincreased by increasing the size of the sample of tags or signaturescounted, e.g. Audic and Claverie (cited above).

Both digital and non-digital hybridization-based assays have beenimplemented using oligonucleotide tags that are hybridized to theircomplements, typically as part of a detection or signal generationschemes that may include solid phase supports, such as microarrays,microbeads, or the like, e.g. Brenner et al, Proc. Natl. Acad. Sci., 97:1665-1670 (2000); Church et al, Science, 240: 185-188 (1988); Chee,Nucleic Acids Research, 19: 3301-3305 (1991); Shoemaker et al., NatureGenetics, 14: 450456 (1996); Wallace, U.S. Pat. No. 5,981,179; Gerry etal, J. Mol. Biol., 292: 251-262 (1999); Fan et al., Genome Research, 10:853-860 (2000); Ye et al., Human Mutation, 17: 305-316 (2001); and thelike. Bacterial transcript imaging by hybridization of total RNA tonucleic acid arrays may be conducted as described in Saizieu et al.,Nature Biotechnology, 16:45-48 (1998). Accessing genetic informationusing high density DNA arrays is further described in Chee et al.,Science 274:610-614 (1996). Tagging approaches have also been used incombination with next-generation sequencing methods, see for example,Smith et al. NAR (May 11, 2010), 1-7.

A common feature among all of these approaches is a one-to-onecorrespondence between probe sequences and oligonucleotide tagsequences. That is, the oligonucleotide tags have been employed as probesurrogates for their favorable hybridizations properties, particularlyunder multiplex assay conditions.

Determining small numbers of biological molecules and their changes isessential when unraveling mechanisms of cellular response,differentiation or signal transduction, and in performing a wide varietyof clinical measurements. Although many analytical methods have beendeveloped to measure the relative abundance of different moleculesthrough sampling (e.g., microarrays and sequencing), few techniques areavailable to determine the absolute number of molecules in a sample.This can be an important goal, for example in single cell measurementsof copy number or stochastic gene expression, and is especiallychallenging when the number of molecules of interest is low in abackground of many other species. As an example, measuring the relativecopy number or expression level of a gene across a wide number of genescan currently be performed using PCR, hybridization to a microarray orby direct sequence counting. PCR and microarray analysis rely on thespecificity of hybridization to identify the target of interest foramplification or capture respectively, then yield an analog signalproportional to the original number of molecules. A major advantage ofthese approaches is in the use of hybridization to isolate the specificmolecules of interest within the background of many other molecules,generating specificity for the readout or detection step. Thedisadvantage is that the readout signal to noise is proportional to allmolecules (specific and non-specific) specified by selectiveamplification or hybridization. The situation is reversed for sequencecounting. No intended sequence specificity is imposed in the sequencecapture step, and all molecules are sequenced. The major advantage isthat the detection step simply yields a digital list of those sequencesfound, and since there is no specificity in the isolation step, allsequences must be analyzed at a sufficient statistical depth in order tolearn about a specific sequence. Although very major technical advancesin sequencing speed and throughput have occurred, the statisticalrequirements imposed to accurately measure small changes inconcentration of a specific gene within the background of many othersequences requires measuring many sequences that don't matter to findthe ones that do matter. Each of these techniques, PCR, arrayhybridization and sequence counting is a comparative technique in thatthey primarily measure relative abundance, and do not typically yield anabsolute number of molecules in a solution. A method of absolutecounting of nucleic acids is digital PCR (B. Vogelstein, K. W. Kinzler,Proc Natl Acad Sci USA 96, 9236 (Aug. 3, 1999)), where solutions areprogressively diluted into individual compartments until there is anaverage probability of one molecule per two wells, then detected by PCR.Although digital PCR can be used as a measure of absolute abundance, thedilutions must be customized for each type of molecule, and thus inpractice is generally limited to the analysis of a small number ofdifferent molecules.

SUMMARY OF THE INVENTION

High-sensitivity single molecule digital counting by the stochasticlabeling of a collection of identical molecules is disclosed. Each copyof a molecule randomly chooses from a non-depleting reservoir of diverselabels. The uniqueness of each labeled molecule is determined by thestatistics of random choice, and depends on the number of copies ofidentical molecules in the collection compared to the diversity oflabels. The size of the resulting set of labeled molecules is determinedby the stochastic nature of the labeling process, and analysis revealsthe original number of molecules. When the number of copies of amolecule to the diversity of labels is low, the labeled molecules arehighly unique, and the digital counting efficiency is high. Thisstochastic transformation relaxes the problem of counting molecules fromone of locating and identifying identical molecules to a series ofyes/no digital questions detecting whether preprogrammed labels arepresent. The conceptual framework for stochastic mapping of a variety ofmolecule types is developed and the utility of the methods aredemonstrated by stochastically labeling 360,000 different fragments ofthe human genome. The labeled fragments for a target molecule of choiceare detected with high specificity using a microarray readout system,and with DNA sequencing. The results are consistent with a stochasticprocess, and yield highly precise relative and absolute countingstatistics of selected molecules within a vast background of othermolecules.

Methods are disclosed herein for digital counting of individualmolecules of one or more targets. In preferred embodiments the targetsare nucleic acids, but may be a variety of biological or non-biologicalelements. Targets are labeled so that individual occurrences of the sametarget are marked by attachment of a different label to differenceoccurrences. The attachment of the label confers a separate,determinable identity to each occurrence of targets that may otherwisebe indistinguishable. Preferably the labels are different sequences thattag or mark each target occurrence uniquely. The resulting modifiedtarget comprises the target sequence and the unique identifier (whichmay be referred to herein as tag, counter, label, or marker). Thejunction of the target and identifier forms a uniquely detectablemechanism for counting the occurrence of that copy of the target. Theattachment of the identifier to each occurrence of the target is arandom sampling event. Each occurrence of target could choose any of thelabels. Each identifier is present in multiple copies so selection ofone copy does not remove that identifier sequence from the pool ofidentifiers so it is possible that the same identifier will be selectedtwice. The probability of that depends on the number of targetoccurrences relative to the number of different identifier sequences.

Each stochastic attachment event, where a target occurrence is attachedto a unique identifier, results in the creation of a novel sequenceformed at the junction of the identifier and the target. For a giventarget, all resulting products will contain the same target portion, buteach will contain a different identifier sequence (T1L1, T1L2, . . .T1LN where N is the number of different occurrences of target1, “T1” andL is the identifier, L1, L2 . . . LN). In preferred aspects theoccurrences are detected by hybridization. In some aspects the methodsand systems include a probe array comprising features, wherein eachfeature has a different combination of target sequence with identifiers,1 to N wherein N is the number of unique identifiers in the pool ofidentifiers. The array has N features for each target, so if there are 8targets to be analyzed there are 8 times N features on the array tointerrogate the 8 targets.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of a method of stochastic labeling and counting byhybridization to an array of support bound probes.

FIG. 2A shows a schematic of labeling target molecules with a pool oflabels.

FIG. 2B shows a schematic of detection of labeled targets on an arrayhaving features that are label specific and target specific.

FIG. 3 shows a schematic of a method for circularizing targets andamplifying with gene specific primers.

FIG. 4 shows a schematic of a method for detection of ligation productsby hybridization to array probes that are complementary to the sequenceresulting from the ligation.

FIG. 5 shows a schematic of a method for target preparation.

FIG. 6 shows a method for stochastic counting by fragmentation where theunique end of the fragment is the label used for counting.

FIG. 7 provides an example of a genomic target ligated at either end toa label adaptor.

FIG. 8 shows a schematic of the arrangement and position of theadaptors, PCR primers, and the biotinylated array-ligation probe in oneexemplary sample prep method.

FIG. 9 is a schematic of a method for using ligation based read out onarrays to detect labeled targets and minimize partial targethybridization.

FIG. 10 shows the arrangement of the adaptors, labels and primers usedto convert the labeled sample into sequencing template.

FIG. 11 is a plot of the number of labels from a non-depleting reservoirof 960 lables that are predicted to be captures at least once, exactlyonce or exactly twice.

FIG. 12 is a plot of counting results for 4 different DNA copy numbertitrations using microarray hybridization (on left) or DNA sequencing in(on right).

FIG. 13 shows relative copy ratios of three tested gene targetsrepresenting copy number 1, 2 or 3 at different dilutions as analyzedusing the disclosed methods.

FIG. 14 shows a comparison between experimentally observed label usagewith those predicted from stochastic modeling.

FIG. 15 shows a plot of the expected label usage (y-axis) when ligatingto a given number of target molecules (x-axis).

FIG. 16 shows a plot of number of target molecules (x-axis) compared tocounting efficiency (y-axis).

FIG. 17 shows a schematic of a method for attaching labels to targetsusing a splint having a variable region.

FIG. 18 shows a schematic of a method for enriching for molecules thatcontain labels, target or both.

FIG. 19 shows a scatter plot of a series of different target plus labelcombinations.

FIG. 20 shows a plot of counting efficiency versus copies of target asthe number of labels varies. The inset is a magnification of the upperleft portion of the graph.

FIG. 21 is a plot of labels the array intensity observed compared to thenumber of fragments when fragments are binned according to size.

FIG. 22 shows labels observed by microarray hybridization plottedagainst intensity (y-axis) for each of 960 labels for the Chr 4 genetarget.

FIG. 23 shows frequency plots (y-axis, log-scale) of intensitydistributions of the 960 labels in the microarray experiments with thecounting threshold applied indicated by the dashed line.

FIG. 24 shows plots showing fragment size distribution and mean rawintensity on chr22 tiling probes on the “CNVtype” array.

FIG. 25 shows a simulated PCR run showing the replication outcome for500 molecules of a target fragment ligated to a library of 960 labelcounters.

FIG. 26 shows intensities of 1,152 array probes associated with a singlegene target on chromosome 4 in the upper panel and a histogram of theintensity data corresponding to 960 labels in the lower panel.

FIG. 27 shows a plot of the number of times each of the 960 labels wasobserved in ligations with low DNA target amounts.

FIG. 28 shows an example of a replication process on a collection of 390uniquely labeled target molecules resulting from 960 diverse labelsindependently marked with 500 copies of a target molecule.

FIG. 29 shows plots of labels observed in the mapped reads from thefirst sequencing run for chromosome 4 with the horizontal dashed lineindicating the counting threshold applied and the vertical dashed lineindicating the break separating the 192 negative controls from theexpected labels (controls to the right of the line).

DETAILED DESCRIPTION OF THE INVENTION

Reference will now be made in detail to exemplary embodiments of theinvention. While the invention will be described in conjunction with theexemplary embodiments, it will be understood that they are not intendedto limit the invention to these embodiments. On the contrary, theinvention is intended to cover alternatives, modifications andequivalents, which may be included within the spirit and scope of theinvention.

The invention has many preferred embodiments and relies on many patents,applications and other references for details known to those of the art.Therefore, when a patent, application, or other reference, such as aprinted publication, is cited or repeated below, it should be understoodthat it is incorporated by reference in its entirety for all purposesand particularly for the proposition that is recited.

As used in this application, the singular form “a,” “an,” and “the”include plural references unless the context clearly dictates otherwise.For example, the term “an agent” includes a plurality of agents,including mixtures thereof.

An individual is not limited to a human being, but may also be otherorganisms including, but not limited to, mammals, plants, bacteria, orcells derived from any of the above.

Throughout this disclosure, various aspects of this invention can bepresented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

The practice of the present invention may employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such conventional techniques includepolymer array synthesis, hybridization, ligation, and detection ofhybridization using a label. Specific illustrations of suitabletechniques can be had by reference to the example herein below. However,other equivalent conventional procedures can, of course, also be used.Such conventional techniques and descriptions can be found in standardlaboratory manuals such as Genome Analysis: A Laboratory Manual Series(Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A LaboratoryManual, PCR Primer: A Laboratory Manual, and Molecular Cloning: ALaboratory Manual (all from Cold Spring Harbor Laboratory Press), Gait,“Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press,London, Nelson and Cox (2000), Lehninger et al., (2008) Principles ofBiochemistry 5th Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al.(2006) Biochemistry, 6^(th) Ed., W. H. Freeman Pub., New York, N.Y., allof which are herein incorporated in their entirety by reference for allpurposes.

The present invention can employ solid substrates, including arrays insome preferred embodiments. Methods and techniques applicable to polymer(including protein) array synthesis have been described in U.S. PatentPub. No. 20050074787, WO 00/58516, U.S. Pat. Nos. 5,143,854, 5,242,974,5,252,743, 5,324,633, 5,384,261, 5,405,783, 5,424,186, 5,451,683,5,482,867, 5,491,074, 5,527,681, 5,550,215, 5,571,639, 5,578,832,5,593,839, 5,599,695, 5,624,711, 5,631,734, 5,795,716, 5,831,070,5,837,832, 5,856,101, 5,858,659, 5,936,324, 5,968,740, 5,974,164,5,981,185, 5,981,956, 6,025,601, 6,033,860, 6,040,193, 6,090,555,6,136,269, 6,269,846 and 6,428,752, in PCT Publication No. WO 99/36760and WO 01/58593, which are all incorporated herein by reference in theirentirety for all purposes.

Patents that describe synthesis techniques in specific embodimentsinclude U.S. Patent Nos. 5,412,087, 6,147,205, 6,262,216, 6,310,189,5,889,165, and 5,959,098. Nucleic acid arrays are described in many ofthe above patents, but the same techniques may be applied to polypeptidearrays.

The present invention also contemplates many uses for polymers attachedto solid substrates. These uses include gene expression monitoring,profiling, library screening, genotyping and diagnostics. Geneexpression monitoring and profiling methods can be shown in U.S. Pat.Nos. 5,800,992, 6,013,449, 6,020,135, 6,033,860, 6,040,138, 6,177,248and 6,309,822. Genotyping and uses therefore are shown in U.S. PatentPublication Nos. 20030036069 and 20070065816 and U.S. Pat. Nos.5,856,092, 6,300,063, 5,858,659, 6,284,460, 6,361,947, 6,368,799 and6,333,179. Other uses are embodied in U.S. Pat. Nos. 5,871,928,5,902,723, 6,045,996, 5,541,061, and 6,197,506.

The present invention also contemplates sample preparation methods incertain embodiments. Prior to or concurrent with analysis, the samplemay be amplified by a variety of mechanisms. In some aspects nucleicacid amplification methods such as PCR may be combined with thedisclosed methods and systems. See, for example, PCR Technology:Principles and Applications for DNA Amplification (Ed. H. A. Erlich,Freeman Press, NY, N.Y., 1992); PCR Protocols: A Guide to Methods andApplications (Eds. Innis, et al., Academic Press, San Diego, Calif.,1990); Mattila et al., Nucleic Acids Res. 19, 4967 (1991); Eckert etal., PCR Methods and Applications 1, 17 (1991); PCR (Eds. McPherson etal., IRL Press, Oxford); and U.S. Pat. Nos. 4,683,202, 4,683,195,4,800,159, 4,965,188, and 5,333,675, each of which is incorporatedherein by reference in their entireties for all purposes. Enzymes andrelated methods of use in molecular biology that may be used incombination with the disclosed methods and systems are reviewed, forexample, in Rittie and Perbal, J. Cell Commun. Signal. (2008) 2:25-45.The sample may be amplified on the array. See, for example, U.S. Pat.No. 6,300,070 and which is incorporated herein by reference in itsentirety for all purposes.

Many of the methods and systems disclosed herein utilize enzymeactivities. A variety of enzymes are well known, have been characterizedand many are commercially available from one or more supplier. For areview of enzyme activities commonly used in molecular biology see, forexample, Rittie and Perbal, J. Cell Commun. Signal. (2008) 2:25-45,incorporated herein by reference in its entirety. Exemplary enzymesinclude

DNA dependent DNA polymerases (such as those shown in Table 1 of Rittieand Perbal), RNA dependent DNA polymerase (see Table 2 of Rittie andPerbal), RNA polymerases, ligases (see Table 3 of Rittie and Perbal),enzymes for phosphate transfer and removal (see Table 4 of Rittie andPerbal), nucleases (see Table 5 of Rittie and Perbal), and methylases.

Other methods of genome analysis and complexity reduction include, forexample, AFLP, see U.S. Pat. No. 6,045,994, which is incorporated hereinby reference, and arbitrarily primed-PCR (AP-PCR) see McClelland andWelsh, in PCR Primer: A laboratory Manual, (1995) eds. C. Dieffenbachand G. Dveksler, Cold Spring Harbor Lab Press, for example, at p 203,which is incorporated herein by reference in its entirety. Additionalmethods of sample preparation and techniques for reducing the complexityof a nucleic sample are described in Dong et al., Genome Research 11,1418 (2001), in U.S. Pat. No 6,361,947, 6,391,592, 6,458,530 and U.S.Patent Publication Nos. 20030039069, 20050079536, 20030096235,20030082543, 20040072217, 20050142577, 20050233354, 20050227244,20050208555, 20050074799, 20050042654 and 20040067493, which are eachincorporated herein by reference in their entireties.

The design and use of allele-specific probes for analyzing polymorphismsis described by e.g., Saiki et al., Nature 324, 163-166 (1986);Dattagupta, EP 235,726, and WO 89/11548. Allele-specific probes can bedesigned that hybridize to a segment of target DNA from one individualbut do not hybridize to the corresponding segment from anotherindividual due to the presence of different polymorphic forms in therespective segments from the two individuals.

Sample preparation methods are also contemplated in many embodiments.Prior to or concurrent with analysis, the genomic sample may beamplified by a variety of mechanisms, some of which may employ PCR. See,e.g., PCR Technology: Principles and Applications for DNA Amplification(Ed. H. A. Erlich, Freeman Press, NY, N.Y., 1992); PCR Protocols: AGuide to Methods and Applications (Eds. Innis, et al., Academic Press,San Diego, Calif., 1990); Mattila et al., Nucleic Acids Res. 19, 4967(1991); Eckert et al., PCR Methods and Applications 1, 17 (1991); PCR(Eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. Nos.4,683,202, 4,683,195, 4,800,159 4,965,188,and 5,333,675, and each ofwhich is incorporated herein by reference in their entireties for allpurposes. See also U.S. Pat. No. 6,300,070 which is incorporated hereinby reference. Additional methods of sample preparation and techniquesfor reducing the complexity of a nucleic sample are described in Dong etal., Genome Research 11, 1418 (2001), in U.S. Pat. No. 6,361,947,6,391,592 and U.S. Patent Pub. Nos. 20030096235, 20030082543 and20030036069.

Other suitable amplification methods include the ligase chain reaction(LCR) (for example, Wu and Wallace, Genomics 4, 560 (1989), Landegren etal., Science 241, 1077 (1988) and Barringer et al. Gene 89:117 (1990)),transcription amplification (Kwoh et al., Proc. Natl. Acad. Sci. USA 86,1173 (1989) and WO88/10315), self-sustained sequence replication(Guatelli et al., Proc. Nat. Acad. Sci. USA, 87, 1874 (1990) andWO90/06995), selective amplification of target polynucleotide sequences(U.S. Pat. No. 6,410,276), consensus sequence primed polymerase chainreaction (CP-PCR) (U.S. Pat. No. 4,437,975), arbitrarily primedpolymerase chain reaction (AP-PCR) (U.S. Pat. Nos. 5, 413,909,5,861,245), rolling circle amplification (RCA) (for example, Fire andXu, PNAS 92:4641 (1995) and Liu et al., J. Am. Chem. Soc. 118:1587(1996)) and nucleic acid based sequence amplification (NABSA). (See,U.S. Pat. Nos. 5,409,818, 5,554,517, and 6,063,603, each of which isincorporated herein by reference). Other amplification methods that maybe used are described in, U.S. Pat. Nos. 6,582,938, 5,242,794,5,494,810, 4,988,617, and US Pub. No. 20030143599 each of which isincorporated herein by reference.

Molecular inversion probes may also be used for amplification ofselected targets. MIPs may be generated so that the ends of thepre-circle probe are complementary to regions that flank the region tobe amplified. The gap can be closed by extension of the end of the probeso that the complement of the target is incorporated into the MIP priorto ligation of the ends to form a closed circle. The closed circle canbe amplified as previously disclosed in Hardenbol et al., Genome Res.15:269-275 (2005) and in U.S. Pat. No. 6,858,412.

In some embodiments, amplification may include the use of a stranddisplacing polymerase that may be primed by selected primers or by amixture of primers, for example, random hexamers. See for example Laskenand Egholm, Trends Biotechnol. 2003 21(12):531-5; Barker et al. GenomeRes. 2004 May;14(5):901-7; Dean et al. Proc Natl Acad Sci USA. 2002;99(8):5261-6; and Paez, J. G., et al. Nucleic Acids Res. 2004;32(9):e71. Other amplification methods that may be used include: QbetaReplicase, described in PCT Patent Application No. PCT/US87/00880,isothermal amplification methods such as SDA, described in Walker et al.1992, Nucleic Acids Res. 20(7):1691-6, 1992, and rolling circleamplification, described in U.S. Pat. No. 5,648,245. DNA may also beamplified by multiplex locus-specific PCR or using adaptor-ligation andsingle primer PCR. Other available methods of amplification, such asbalanced PCR (Makrigiorgos, et al. (2002), Nat Biotechnol, Vol. 20,pp.936-9), may also be used.

Methods of ligation will be known to those of skill in the art and aredescribed, for example in Sambrook et at. (2001) and the New EnglandBioLabs catalog both of which are incorporated herein by reference forall purposes. Methods include using T4 DNA Ligase which catalyzes theformation of a phosphodiester bond between juxtaposed 5′phosphate and3′hydroxyl termini in duplex DNA or RNA with blunt and sticky ends; TaqDNA Ligase which catalyzes the formation of a phosphodiester bondbetween juxtaposed 5′phosphate and 3′hydroxyl termini of two adjacentoligonucleotides which are hybridized to a complementary target DNA; E.coli DNA ligase which catalyzes the formation of a phosphodiester bondbetween juxtaposed 5′-phosphate and 3′-hydroxyl termini in duplex DNAcontaining cohesive ends; and T4 RNA ligase which catalyzes ligation ofa 5′phosphoryl-terminated nucleic acid donor to a 3′hydroxyl-terminatednucleic acid acceptor through the formation of a 3′->5′phosphodiesterbond, substrates include single-stranded RNA and DNA as well asdinucleoside pyrophosphates; or any other methods described in the art.Fragmented DNA may be treated with one or more enzymes, for example, anendonuclease, prior to ligation of adaptors to one or both ends tofacilitate ligation by generating ends that are compatible withligation.

Fixed content mapping arrays are available from Affymetrix, for example,the SNP 6.0 array. Methods for using mapping arrays see, for example,Kennedy et al., Nat. Biotech. 21:1233-1237 (2003), Matsuzaki et al.,Genome Res. 14:414-425 (2004), Matsuzaki et al., Nat. Meth. 1:109-111(2004) and U.S. Patent Pub. Nos. 20040146890 and 20050042654, eachincorporated herein by reference. Applications of microarrays for SNPgenotyping have been described in e.g., U.S. Pat. Nos 6,300,063,6,361,947, 6,368,799 and US Patent Publication Nos. 20040067493,20030232353, 20030186279, 20050260628, 20070065816 and 20030186280, allincorporated herein by reference in their entireties for all purposes.

Selected panels of SNPs can also be interrogated using a panel of locusspecific probes in combination with a universal array as described inHardenbol et al., Genome Res. 15:269-275 (2005) and in U.S. Pat. No.6,858,412. Universal tag arrays and reagent kits for performing suchlocus specific genotyping using panels of custom molecular inversionprobes (MIPs) are available from Affymetrix.

Computer implemented methods for determining genotype using data frommapping arrays are disclosed, for example, in Liu, et al.,Bioinformatics 19:2397-2403 (2003), Rabbee and Speed, Bioinformatics,22:7-12 (2006), and Di et al., Bioinformatics 21:1958-63 (2005).Computer implemented methods for linkage analysis using mapping arraydata are disclosed, for example, in Ruschendorf and Nurnberg,Bioinformatics 21:2123-5 (2005) and Leykin et al., BMC Genet. 6:7,(2005). Computer methods for analysis of genotyping data are alsodisclosed in U.S. Patent Pub. Nos. 20060229823, 20050009069,20040138821, 20060024715, 20050250151 and 20030009292.

Methods for analyzing chromosomal copy number using mapping arrays aredisclosed, for example, in Bignell et al., Genome Res. 14:287-95 (2004),Lieberfarb, et al., Cancer Res. 63:4781-4785 (2003), Zhao et al., CancerRes. 64:3060-71 (2004), Huang et al., Hum Genomics 1:287-299 (2004),Nannya et al., Cancer Res. 65:6071-6079 (2005), Slater et al., Am. J.Hum. Genet. 77:709-726 (2005) and Ishikawa et al., Biochem. and Biophys.Res. Comm., 333:1309-1314 (2005). Computer implemented methods forestimation of copy number based on hybridization intensity are disclosedin U.S. Patent Pub. Nos. 20040157243, 20050064476, 20050130217,20060035258, 20060134674 and 20060194243.

Additional methods of sample preparation and techniques for reducing thecomplexity of a nucleic sample are described in Dong et al., GenomeResearch 11, 1418 (2001), in U.S. Pat. Nos. 6,361,947, 6,391,592 and6,872,529 and U.S. Patent Publication Nos. 20030036069, 20030096235 and20030082543. Additional methods of using a genotyping array aredisclosed, for example, in U.S. Patent Publication Nos. 20040146883,20030186280, 20030186279, 20040067493, 20030232353, 20060292597,20050233354, 20050074799, 20070065816 and 20040185475.

Methods for conducting polynucleotide hybridization assays have beenwell developed in the art. Hybridization assay procedures and conditionswill vary depending on the application and are selected in accordancewith known general binding methods, including those referred to in:Maniatis et al. Molecular Cloning: A Laboratory Manual (2^(nd) Ed. ColdSpring Harbor, N.Y., 1989); Berger and Kimmel Methods in Enzymology,Vol. 152, Guide to Molecular Cloning Techniques (Academic Press, Inc.,San Diego, Calif., 1987); Young and Davis, P.N.A.S, 80: 1194 (1983).Methods and apparatus for carrying out repeated and controlledhybridization reactions have been described in U.S. Pat. Nos. 5,871,928,5,874,219, 6,045,996 and 6,386,749, 6,391,623 each of which areincorporated herein by reference.

The present invention also contemplates signal detection ofhybridization between ligands in certain preferred embodiments. See U.S.Pat. Nos. 5,143,854, 5,578,832, 5,631,734, 5,834,758, 5,936,324,5,981,956, 6,025,601, 6,141,096, 6,185,030, 6,201,639, 6,218,803, and6,225,625 in U.S. Patent Pub. No. 20040012676 and in PCT ApplicationPCT/US99/06097 (published as WO99/47964), each of which also is herebyincorporated by reference in its entirety for all purposes.

Methods and apparatus for signal detection and processing of intensitydata are disclosed in, for example, U.S. Pat. Nos. 5,143,854, 5,547,839,5,578,832, 5,631,734, 5,800,992, 5,834,758, 5,856,092, 5,902,723,5,936,324, 5,981,956, 6,025,601, 6,090,555, 6,141,096, 6,185,030,6,201,639; 6,218,803; and 6,225,625, in U.S. Patent Pub. Nos.20040012676 and 20050059062 and in PCT Application PCT/US99/06097(published as WO99/47964), each of which also is hereby incorporated byreference in its entirety for all purposes.

The practice of the present invention may also employ conventionalbiology methods, software and systems. Computer software products of theinvention typically include computer readable medium havingcomputer-executable instructions for performing the logic steps of themethod of the invention. Suitable computer readable medium includefloppy disk, CD-ROM/DVD/DVD-ROM, hard-disk drive, flash memory, ROM/RAM,magnetic tapes, etc. The computer-executable instructions may be writtenin a suitable computer language or combination of several languages.Basic computational biology methods are described in, for example,Setubal and Meidanis et al., Introduction to Computational BiologyMethods (PWS Publishing Company, Boston, 1997); Salzberg, Searles,Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier,Amsterdam, 1998); Rashidi and Buehler, Bioinformatics Basics:Application in Biological Science and Medicine (CRC Press, London, 2000)and Ouelette and Bzevanis Bioinformatics: A Practical Guide for Analysisof Gene and Proteins (Wiley & Sons, Inc., 2^(nd) ed., 2001). See U.S.Pat. No. 6,420,108.

The present invention may also make use of various computer programproducts and software for a variety of purposes, such as probe design,management of data, analysis, and instrument operation. See, U.S. Pat.Nos. 5,593,839, 5,795,716, 5,733,729, 5,974,164, 6,066,454, 6,090,555,6,185,561, 6,188,783, 6,223,127, 6,229,911 and 6,308,170. Computermethods related to genotyping using high density microarray analysis mayalso be used in the present methods, see, for example, US Patent Pub.Nos. 20050250151, 20050244883, 20050108197, 20050079536 and 20050042654.

Additionally, the present disclosure may have preferred embodiments thatinclude methods for providing genetic information over networks such asthe Internet as shown in U.S. Patent Pub. Nos. 20030097222, 20020183936,20030100995, 20030120432, 20040002818, 20040126840, and 20040049354.

An allele refers to one specific form of a genetic sequence (such as agene) within a cell, an individual or within a population, the specificform differing from other forms of the same gene in the sequence of atleast one, and frequently more than one, variant sites within thesequence of the gene. The sequences at these variant sites that differbetween different alleles are termed “variances”, “polymorphisms”, or“mutations”. At each autosomal specific chromosomal location or “locus”an individual possesses two alleles, one inherited from one parent andone from the other parent, for example one from the mother and one fromthe father. An individual is “heterozygous” at a locus if it has twodifferent alleles at that locus. An individual is “homozygous” at alocus if it has two identical alleles at that locus.

Single nucleotide polymorphisms (SNPs) are positions at which twoalternative bases occur at appreciable frequency (>1%) in a givenpopulation. SNPs are a common type of human genetic variation and areuseful in the performance of genome wide association studies (GWAS).GWAS may be used, for example for the analysis of biological pathways,see Wang and Hakonarson, Nat. Rev. Genet. 2010, 11:843-854. Other commonvariation includes single base deletions or insertions of a nucleotiderelative to a reference allele. Copy number variants (CNVs),transversions and other rearrangements are also forms of geneticvariation.

The term genotyping refers to the determination of the geneticinformation an individual carries at one or more positions in thegenome. For example, genotyping may comprise the determination of whichallele or alleles an individual carries for a single SNP or thedetermination of which allele or alleles an individual carries for aplurality of SNPs or CNVs. A diploid individual may be homozygous foreach of the two possible alleles (for example, AA or BB) or heterozygous(for example, AB). For additional information regarding genotyping andgenome structure see, Color Atlas of Genetics, Ed. Passarge, Thieme, NewYork, N.Y. (2001), which is incorporated by reference.

Normal cells that are heterozygous at one or more loci may give rise totumor cells that are homozygous at those loci. This loss ofheterozygosity (LOH) may result from structural deletion of normal genesor loss of the chromosome carrying the normal gene, mitoticrecombination between normal and mutant genes, followed by formation ofdaughter cells homozygous for deleted or inactivated (mutant) genes; orloss of the chromosome with the normal gene and duplication of thechromosome with the deleted or inactivated (mutant) gene.

The term “array” as used herein refers to an intentionally createdcollection of molecules which can be prepared either synthetically orbiosynthetically. The molecules in the array can be identical ordifferent from each other. The array can assume a variety of formats,for example, libraries of soluble molecules; libraries of compoundstethered to resin beads, silica chips, microparticles, nanoparticles orother solid supports.

The term “complementary” as used herein refers to the hybridization orbase pairing between nucleotides or nucleic acids, such as, forinstance, between the two strands of a double stranded DNA molecule orbetween an oligonucleotide primer and a primer binding site on a singlestranded nucleic acid to be sequenced or amplified. See, M. KanehisaNucleic Acids Res. 12:203 (1984), incorporated herein by reference.

The term “copy number variation” or “CNV” refers to differences in thecopy number of genetic information. In many aspects it refers todifferences in the per genome copy number of a genomic region. Forexample, in a diploid organism the expected copy number for autosomalgenomic regions is 2 copies per genome. Such genomic regions should bepresent at 2 copies per cell. For a recent review see Zhang et al. Annu.Rev. Genomics Hum. Genet. 2009. 10:451-81. CNV is a source of geneticdiversity in humans and can be associated with complex disorders anddisease, for example, by altering gene dosage, gene disruption, or genefusion. They can also represent benign polymorphic variants. CNVs can belarge, for example, larger than 1 Mb, but many are smaller, for examplebetween 100 by and 1 Mb. More than 38,000 CNVs greater than 100 by (andless than 3 Mb) have been reported in humans. Along with SNPs these CNVsaccount for a significant amount of phenotypic variation betweenindividuals. In adition to having deleterious impacts, e.g. causingdisease, they may also result in advantageous variation.

Digital PCR is a technique where a limiting dilution of the sample ismade across a large number of separate PCR reactions so that most of thereactions have no template molecules and give a negative amplificationresult. Those reactions that are positive at the reaction endpoint arecounted as individual template molecules present in the original samplein a 1 to 1 relationship. See Kalina et al. NAR 25:1999-2004 (1997) andVogelstein and Kinzler, PNAS 96:9236-9241 (1999). This method is anabsolute counting method where solutions are partitioned into containersuntil there is an average probability of one molecule per two containersor when, P₀=(1−e^(−n/c))=½; where n is the number of molecules and c isthe number of containers, or n/c is 0.693. Quantitative partitioning isassumed, and the dynamic range is governed by the number of containersavailable for stochastic separation. The molecules are then detected byPCR and the number of positive containers is counted. Each successfulamplification is counted as one molecule, independent of the actualamount of product. PCR-based techniques have the additional advantage ofonly counting molecules that can be amplified, e.g. that are relevant tothe massively parallel PCR step in the sequencing workflow. Becausedigital PCR has single molecule sensitivity, only a few hundred librarymolecules are required for accurate quantification. Elimination of thequantification bottleneck reduces the sample input requirement frommicrograms to nanograms or less, opening the way for minute and/orprecious samples onto the next-generation sequencing platforms withoutthe distorting effects of pre-amplification. Digital PCR has been usedto quantify sequencing libraries to eliminate uncertainty associatedwith the construction and application of standard curves to PCR-basedquantification and enable direct sequencing without titration runs. SeeWhite et al. BMC Genomics 10: 116 (2009).

To vary dynamic range, micro-fabrication can be used to substantiallyincrease the number of containers. See, Fan et al. Am J Obstet Gynecol200, 543 el (May, 2009).

Similarly, in stochastic labeling as disclosed herein, the samestatistical conditions are met when P₀=(1−e^(−n/m))=½; where m is thenumber of labels, and one half of the labels will be used at least oncewhen n/m =0.693. The dynamic range is governed by the number of labelsused, and the number of labels can be easily increased to extend thedynamic range. The number of containers in digital PCR plays the samerole as the number of labels in stochastic labeling and by substitutingcontainers for labels identical statistical equations may be applied.Using the principles of physical separation, digital PCR stochasticallyexpands identical molecules into physical space, whereas the principlegoverning stochastic labeling is identity based and expands identicalmolecules into identity space.

The term “hybridization” as used herein refers to the process in whichtwo single-stranded polynucleotides bind noncovalently to form a stabledouble-stranded polynucleotide; triple-stranded hybridization is alsotheoretically possible. The resulting (usually) double-strandedpolynucleotide is a “hybrid.” The proportion of the population ofpolynucleotides that forms stable hybrids is referred to herein as the“degree of hybridization.” Hybridizations may be performed understringent conditions, for example, at a salt concentration of no morethan 1 M and a temperature of at least 25° C. For example, conditions of5×SSPE (750 mM NaCl, 50 mM NaPhosphate, 5 mM EDTA, pH 7.4) and atemperature of 25-30° C. are suitable for allele-specific probehybridizations. For stringent conditions, see, for example, Sambrook,Fritsche and Maniatis. “Molecular Cloning A laboratory Manual” 2^(nd)Ed. Cold Spring Harbor Press (1989) which is hereby incorporated byreference in its entirety for all purposes above. In some aspects saltconcentrations for hybridization are preferably between about 200 mM andabout 1M or between about 200 mM and about 500 mM. Hybridizationtemperatures can be as low as 5° C. , but are typically greater than 22°C., more typically greater than about 30° C., and preferably in excessof about 37° C. Longer fragments may require higher hybridizationtemperatures for specific hybridization. As other factors may affect thestringency of hybridization, including base composition and length ofthe complementary strands, presence of organic solvents and extent ofbase mismatching, the combination of parameters is more important thanthe absolute measure of any one alone.

The term “mRNA” or sometimes refer by “mRNA transcripts” as used herein,include, but not limited to pre-mRNA transcript(s), transcriptprocessing intermediates, mature mRNA(s) ready for translation andtranscripts of the gene or genes, or nucleic acids derived from the mRNAtranscript(s). Transcript processing may include splicing, editing anddegradation. As used herein, a nucleic acid derived from an mRNAtranscript refers to a nucleic acid for whose synthesis the mRNAtranscript or a subsequence thereof has ultimately served as a template.Thus, a cDNA reverse transcribed from an mRNA, an RNA transcribed fromthat cDNA, a DNA amplified from the cDNA, an RNA transcribed from theamplified DNA, etc., are all derived from the mRNA transcript anddetection of such derived products is indicative of the presence and/orabundance of the original transcript in a sample. Thus, mRNA derivedsamples include, but are not limited to, mRNA transcripts of the gene orgenes, cDNA reverse transcribed from the mRNA, cRNA transcribed from thecDNA, DNA amplified from the genes, RNA transcribed from amplified DNA,and the like.

The term “nucleic acid” as used herein refers to a polymeric form ofnucleotides of any length, either ribonucleotides, deoxyribonucleotidesor peptide nucleic acids (PNAs), that comprise purine and pyrimidinebases, or other natural, chemically or biochemically modified,non-natural, or derivatized nucleotide bases. The backbone of thepolynucleotide can comprise sugars and phosphate groups, as maytypically be found in RNA or DNA, or modified or substituted sugar orphosphate groups. A polynucleotide may comprise modified nucleotides,such as methylated nucleotides and nucleotide analogs. The sequence ofnucleotides may be interrupted by non-nucleotide components. Thus theterms nucleoside, nucleotide, deoxynucleoside and deoxynucleotidegenerally include analogs such as those described herein. These analogsare those molecules having some structural features in common with anaturally occurring nucleoside or nucleotide such that when incorporatedinto a nucleic acid or oligonucleoside sequence, they allowhybridization with a naturally occurring nucleic acid sequence insolution. Typically, these analogs are derived from naturally occurringnucleosides and nucleotides by replacing and/or modifying the base, theribose or the phosphodiester moiety. The changes can be tailor made tostabilize or destabilize hybrid formation or enhance the specificity ofhybridization with a complementary nucleic acid sequence as desired.

The term “oligonucleotide” or sometimes refer by “polynucleotide” asused herein refers to a nucleic acid ranging from at least 2, preferableat least 8, and more preferably at least 20 nucleotides in length or acompound that specifically hybridizes to a polynucleotide.Polynucleotides of the present invention include sequences ofdeoxyribonucleic acid (DNA) or ribonucleic acid (RNA) which may beisolated from natural sources, recombinantly produced or artificiallysynthesized and mimetics thereof. A further example of a polynucleotideof the present invention may be peptide nucleic acid (PNA). Theinvention also encompasses situations in which there is a nontraditionalbase pairing such as Hoogsteen base pairing which has been identified incertain tRNA molecules and postulated to exist in a triple helix.“Polynucleotide” and “oligonucleotide” are used interchangeably in thisapplication.

The term “polymorphism” as used herein refers to the occurrence of twoor more genetically determined alternative sequences or alleles in apopulation. A polymorphic marker or site is the locus at whichdivergence occurs. Preferred markers have at least two alleles, eachoccurring at frequency of greater than 1%, and more preferably greaterthan 10% or 20% of a selected population. A polymorphism may compriseone or more base changes, an insertion, a repeat, or a deletion. Apolymorphic locus may be as small as one base pair. Polymorphic markersinclude restriction fragment length polymorphisms, variable number oftandem repeats (VNTR's), hypervariable regions, minisatellites,dinucleotide repeats, trinucleotide repeats, tetranucleotide repeats,simple sequence repeats, and insertion elements such as Alu. The firstidentified allelic form is arbitrarily designated as the reference formand other allelic forms are designated as alternative or variantalleles. The allelic form occurring most frequently in a selectedpopulation is sometimes referred to as the wildtype form. Diploidorganisms may be homozygous or heterozygous for allelic forms. Adiallelic polymorphism has two forms. A triallelic polymorphism hasthree forms. Single nucleotide polymorphisms (SNPs) are included inpolymorphisms.

The term “primer” as used herein refers to a single-strandedoligonucleotide capable of acting as a point of initiation fortemplate-directed DNA synthesis under suitable conditions for example,buffer and temperature, in the presence of four different nucleosidetriphosphates and an agent for polymerization, such as, for example, DNAor RNA polymerase or reverse transcriptase. The length of the primer, inany given case, depends on, for example, the intended use of the primer,and generally ranges from 15 to 30 nucleotides. Short primer moleculesgenerally require cooler temperatures to form sufficiently stable hybridcomplexes with the template. A primer need not reflect the exactsequence of the template but must be sufficiently complementary tohybridize with such template. The primer site is the area of thetemplate to which a primer hybridizes. The primer pair is a set ofprimers including a 5′ upstream primer that hybridizes with the 5′ endof the sequence to be amplified and a 3′ downstream primer thathybridizes with the complement of the 3′ end of the sequence to beamplified.

The term “probe” as used herein refers to a surface-immobilized moleculethat can be recognized by a particular target. See U.S. Pat. No.6,582,908 for an example of arrays having all possible combinations ofprobes with 10, 12, and more bases. Examples of probes that can beinvestigated by this invention include, but are not restricted to,agonists and antagonists for cell membrane receptors, toxins and venoms,viral epitopes, hormones (for example, opioid peptides, steroids, etc.),hormone receptors, peptides, enzymes, enzyme substrates, cofactors,drugs, lectins, sugars, oligonucleotides, nucleic acids,oligosaccharides, proteins, and monoclonal antibodies.

The term “solid support”, “support”, and “substrate” as used herein areused interchangeably and refer to a material or group of materialshaving a rigid or semi-rigid surface or surfaces. In many embodiments,at least one surface of the solid support will be substantially flat,although in some embodiments it may be desirable to physically separatesynthesis regions for different compounds with, for example, wells,raised regions, pins, etched trenches, or the like. According to otherembodiments, the solid support(s) will take the form of beads, resins,gels, microspheres, or other geometric configurations. See U.S. Pat. No.5,744,305 and US Patent Pub. Nos. 20090149340 and 20080038559 forexemplary substrates.

A stochastic process is the counterpart to a deterministic process.Instead of dealing with only one possible “reality” of how the processmight evolve under time, in a stochastic or random process there is someindeterminacy in its future evolution described by probabilitydistributions. This means that even if the initial condition (orstarting point) is known, there are many possibilities the process mightgo to, but some paths are more probable and others less.

In the simplest possible case, a stochastic process amounts to asequence of random variables known as a time series (for example, seeMarkov chain). Another basic type of a stochastic process is a randomfield, whose domain is a region of space, in other words, a randomfunction whose arguments are drawn from a range of continuously changingvalues. One approach to stochastic processes treats them as functions ofone or several deterministic arguments (“inputs”, in most cases regardedas “time”) whose values (“outputs”) are random variables:non-deterministic (single) quantities which have certain probabilitydistributions. Random variables corresponding to various times (orpoints, in the case of random fields) may be completely different. Themain requirement is that these different random quantities all have thesame “type”. Although the random values of a stochastic process atdifferent times may be independent random variables, in most commonlyconsidered situations they exhibit complicated statistical correlations.

Familiar examples of processes modeled as stochastic time series includestock market and exchange rate fluctuations, signals such as speech,audio and video, medical data such as a patient's EKG, EEG, bloodpressure or temperature, and random movement such as Brownian motion orrandom walks. Examples of random fields include static images, randomterrain (landscapes), or composition variations of an heterogeneousmaterial.

The stochastic labeling process can be generalized as follows. Considern copies of a given target molecule T, where T={t_(i), i=1,2, . . . ,n}, and a non-depleting reservoir of m diverse labels L, where L={l_(j),j=1,2, . . . , m}. T reacts with L stochastically, such that each t_(i)will choose exactly one l_(j(i)), 1≦j(i)≦m to take on a new identityt_(i)l_(j(i)), and may be identified by its label subscript. Therefore,the new collection of molecules T* may be denoted as T*={tl_(j(i)),i=1,2, . . . , n, 1≦j(i)≦m}.

When different copies of the target molecules react with the same label,j(i) for those molecules will assume the same value, therefore, thenumber of uniquely labeled target molecules k cannot be greater than m.The stochastic mapping of the set of labels on a target may be describedby a stochastic operator S with m members, acting upon a targetpopulation of n, such that S(m)T(n)=T*(m, n) generating the setT*={tl_(j(i)), i=1,2, . . . , n, 1≦j(i)≦m}. For simplicity, we may writeT*={tl_(k)}. Furthermore, since S operates on all molecules randomly, itwill independently act on many different target sequences and the methodcan be expanded to count copies of multiple target sequences, w,

-   simultaneously:-   ST^(w)=ST₁+ST₂+ . . . +ST_(w)=T₁*+T₂*+ . . .    +T_(w)*={tl_(k)}₁+{tl_(k)}₂+ . . . +{tl_(k)}_(w), where each T_(i)*,    i =1,2, . . . , w consists of a set {tl_(k)}_(i). The net result of    S operating on a specific target population is to map the number of    molecules, n, of that target, to the number of labels captured, k,    which is a random variable.

Since target molecules randomly react with a label with probability

$\frac{1}{m},$the probability of a label being captured by exactly x out of n copiesof a target molecule can be modeled as a Binomial distribution,

${{P(x)} = {\frac{n!}{{x!}{( {n - x} )!}}( \frac{1}{m} )^{x}( {1 - \frac{1}{m}} )^{n - x}}},$where x! denotes the factorial of x. The probability that a label willnot be captured by any copy of the target molecule is P(0)=(1−1/m)^(n),and the probability that a label will be captured at least once is1−P(0) . When n→∞ and 1/m→0 in the way that n/m→λ, P(x) converges to thePoisson distribution with mean 2 , i.e.,

${P(x)} = {\frac{\lambda^{x}}{x!}{{\mathbb{e}}^{- \lambda}.}}$

To compute the number of unique counters captured by n copies of atarget molecule, we introduce an index random variable, X_(i) , which is1 if a counter has been captured at least once, and 0 otherwise. Thenumber of unique counters captured is thus

$k = {\sum\limits_{i = 1}^{m}\;{X_{i}.}}$The mean and variance of k can be derived,

$\begin{matrix}{{E\lbrack k\rbrack} = {m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}} & (1) \\{{{Var}\lbrack k\rbrack} = {{{m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}( {1 - \frac{1}{m}} )^{n}} + {{m( {m - 1} )}\lbrack {( {1 - \frac{2}{m}} )^{n} - ( {1 - \frac{1}{m}} )^{2n}} \rbrack}}} & (2)\end{matrix}$

To compute the number of unique labels captured by n copies of a targetmolecule, we introduce an index random variable, X_(i), which is 1 if alabel has been captured at least once, and 0 otherwise. The number ofunique labels captured is thus

$k = {\sum\limits_{i = 1}^{m}\;{X_{i}.}}$The mean and variance of k can be derived,

$\begin{matrix}{{E\lbrack k\rbrack} = {m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}} & (1) \\{{{Var}\lbrack k\rbrack} = {{{m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}( {1 - \frac{1}{m}} )^{n}} + {{m( {m - 1} )}\lbrack {( {1 - \frac{2}{m}} )^{n} - ( {1 - \frac{1}{m}} )^{2n}} \rbrack}}} & (2)\end{matrix}$

Similarly, to compute the number of labels captured by exactly x copiesof a target molecule, we introduce another index random variable, Y_(i),which is 1 if a label has been captured exactly x times, and 0otherwise. The number of labels captured x times is thus

$t = {\sum\limits_{i = 1}^{m}\;{Y_{i}.}}$The mean and variance of t are,

$\begin{matrix}{{E\lbrack t\rbrack} = {\frac{m \cdot {n!}}{{x!}{( {n - x} )!}}( \frac{1}{m} )^{x}( {1 - \frac{1}{m}} )^{n - x}}} & (3) \\{{{Var}\lbrack t\rbrack} = {{A( {1 - A} )} + {( {m - 1} ){m \cdot \begin{pmatrix}n \\{2x}\end{pmatrix} \cdot ( \frac{2}{m} )^{2x}}( {1 - \frac{2}{m}} )^{n - {2x}}\begin{pmatrix}{2x} \\x\end{pmatrix}( \frac{1}{2} )^{2x}}}} & (4)\end{matrix}$where

${A = {{m \cdot \begin{pmatrix}n \\x\end{pmatrix}}( \frac{1}{m} )^{x}( {1 - \frac{1}{m}} )^{n - x}}},$and the combination

$\begin{pmatrix}n \\x\end{pmatrix} = {\frac{n!}{{x!}{( {n - x} )!}}.}$

The equations were experimentally validated by performing numericalsimulations with 5000 independent runs for each simulated case. Completeagreement with the analytical solutions was observed.

Stochastic Labeling of Individual Molecules

Methods are disclosed herein that may be applied to determining smallnumbers of biological molecules and their changes in response to, forexample, cellular response, differentiation or signal transduction. Themethods may also be used in performing a wide variety of clinicalmeasurements. Although many analytical methods have been developed tomeasure the relative abundance of different molecules through sampling(e.g., microarrays and sequencing), the methods disclosed herein areable to determine the absolute number of molecules in a sample.

Methods for performing single molecule digital counting by thestochastic labeling of a collection of identical molecules aredisclosed. As illustrated in FIGS. 1, 2A and 2B, each copy of a molecule(from a collection of identical target molecules 103) randomly capturesa label by choosing from a large, non-depleting reservoir of diverselabels 101. The uniqueness of each labeled molecule is governed by thestatistics of random choice, and depends on the number of copies ofidentical molecules in the collection compared to the diversity oflabels. Once the molecules are labeled each has been given a uniqueidentity and can now be separately detected. In some aspects, it ispreferable to first amplify the labeled targets prior to detection sothat simple present/absent threshold detection methods can be used.Counting the number of labels is used to determine the original numberof molecules in solution. In some aspects, the molecules to be countedare each members of a class that shares some common feature, forexample, they may each be a single copy of a particular gene sequence ornucleic acid sequence. Counting may be applied, for example, to mRNAtargets, splice products, alternatively spliced products, structuralRNAs, tRNA, miRNA, siRNA, microRNA and the like. Similarly, counting maybe applied to DNA, for example, gene copy number, chromosome number,mitochondrial DNA, bacterial genomes, pathogen nucleic acid, viralnucleic acids and the like. Counting may be applied in research ofdisease in humans or other mammals or agricultural organisms, e.g.cattle, chicken, wheat, rice, fish, etc. Counting may also be applied tocounting aspects of microbes, such as environmental measurements, e.g.water quality testing. The methods may be particularly useful wheresmall numbers of items are to be counted and an accurate count isdesirable rather than a relative estimate.

One embodiment is illustrated schematically in FIG. 1. The library ofdifferent label-tag sequences 101 is combined with a sample thatincludes an unknown number of targets of interest 103. Three differentspecies of target are shown, 103 a, 103 b and 103 c, present at 4, 6 and3 copies respectively. The individual label-tag oligonucleotides fromlibrary 101 are covalently attached to the different targets to formtarget-label-tag molecules 105. Each target has a collection ofdifferent label-tag molecules 105 a, 105 b and 105 c and within eachtarget-specific collection the members differ in the label-tag oligothat is attached. On the array 107, each target is tiled in combinationwith all possible label-tag combinations represented with each differentcombination being present at a different known or determinable locationon the array. In the figure each different possible combination oftarget and label-tag is represented by a single probe for illustrationpurposes, but on the array each different probe is preferably present ina feature having multiple copies of the same probe sequence. The arrayis divided into subarrays 107 a, 107 b and 107 c for illustrativepurposes. The upper portion 109 of the probes varies at each featureaccording to the different label-tag. The lower portion 113 is the samefor all features of each subarray and is complementary to the target.After hybridization individual features of the array are labeled throughhybridization of the complementary target-label-tag molecule to thefeature. The figure shows a detectable label 111 may be used to detectfeatures where a target-label-tag is hybridized.

FIG. 2A illustrates the attachment of different labels from the pool 101to each of 4 different copies of the same target “t”. Label 20 isattached to t1, label 107 to t2, label 477 to t3 and label 9 to t4. Thelabeled targets are then amplified to generate four unique populations,each population representing a single occurrence of the target in thestarting sample.

FIG. 2B illustrates the method for a comparison of two samples, sample 1and 2. The target 201 Gene A is present in 2 copies in sample 1 and 9copies in sample 2. Both samples have non-target molecules 203. Thelabels 205 are combined with the samples and target molecules areattached to individual label-tag molecules in a stochastic manner. Thetargets with attached label-tags are hybridized to an array 211 havingmany features, there is a feature for each possible target-label-tagcombination. Some of the features are labeled, for example, 209 andothers are not, for example, 207. The labeled features indicate thepresence of a specific target-label-tag combination and each correspondsto a count. As shown for gene A in sample 1 there are two labeledfeatures so the count is 2. For Gene A in sample 2 there are 9 labeledfeatures so the count is 9.

The stochastic labeling process can be generalized as follows forillustrative purposes. Consider a given target sequence defined asT={t₁, t₂ . . . t_(n)}; where n is the number of copies of T. A set oflabels is defined as L={l₁, l₂ . . . l_(m)}; where m is the number ofdifferent labels. T reacts stochastically with L, such that each tbecomes attached to one l. If the l's are in non-depleting excess, eacht will choose one l randomly, and will take on a new identityl_(i)t_(j); where l_(i) is chosen from L and j is the j^(th) copy fromthe set of n molecules. We identify each new molecule l_(i)t_(j) by itslabel subscript and drop the subscript for the copies of T, because theyare identical. The new collection of molecules becomes T*=l₁t+l₂t+ . . .l_(i)t; where l_(i) is the i^(th) choice from the set of m labels. It isimportant to emphasize that the subscripts of l at this point refer onlyto the i^(th) choice and provide no information about the identity ofeach l. In fact, l₁ and l₂ will have some probability of beingidentical, depending upon the diversity m of the set of labels. Overall,T* will contain a set of k unique labels resulting from n targetschoosing from the non-depleting reservoir of m labels. Or,T*(m,n)={tl_(k)}; where k represents the number of unique labels thathave been captured. In all cases, k will be smaller than m, approachingm only when n becomes very large. We can define the stochasticattachment of the set of labels on a target using a stochastic operatorS with m members, acting upon a target population of n, such thatS(m)T(n)=T*(m,n) generating the set {tl_(k)}. Furthermore, since Soperates on all molecules randomly, it can independently act on manydifferent target sequences. Hence, the method can simultaneously countcopies of multiple target sequences. The distribution of outcomesgenerated by the number of trials n, from a diversity of m, can beapproximated by the Poisson equation, P_(x)=^(x)/x!e^(−(n/m)). P₀ is theprobability that a label will not be chosen in n trials, and therefore,1−P₀ is the probability that a label will occur at least once. Itfollows that the number of unique labels captured is given by:k=m(1−P₀)=m(1−e^(−(n/m))).

Given k, we can calculate n. In addition to using the Poissonapproximation, the relationship for k, n and m can be describedanalytically using the binomial distribution, or simulated using arandom number generator, each yielding similar results (see SOM).

The outcome of stochastic labeling is illustrated by examining the graphof k verses n (curve 3201 in FIG. 11) calculated using a label diversity(m) of 960. As expected, the number of unique labels captured depends onthe ratio of molecules to labels, n/m. When n is much smaller than m,each molecule almost always captures a unique label, and counting k isequivalent to counting n. As n increases, k increases more slowly asgiven by eq. 1, and yet remains a very precise estimate of n. Forexample, when n/m is ˜0.01, the ratio of unique labels to molecules k/n˜0.99, and we expect an increase of 10 molecules will generate 10+/−Xnew labels. As n/m approaches 0.5 (i.e., ˜480 molecules reacted with 960labels) , k/n˜0.79 and ˜6+/−X new labels are expected with an increaseof 10 molecules. At high n/m, k increases more slowly as labels in thelibrary are more likely to be captured more than once. Curve 3202 inFIG. 11 shows the number of labels chosen exactly once, and curve 3203shows the number of labels chosen exactly twice as n increases. Curve3201 shows the number of labels captured at least once. A more completedescription of the number of times a label is chosen as a function of nis shown in FIG. 15.

The methods and examples below demonstrate that a population ofindistinguishable molecules can be stochastically expanded to apopulation of uniquely identifiable and countable molecules.High-sensitivity threshold detection of single molecules isdemonstrated, and the process can be used to count both the absolute andrelative number of molecules in a sample. The method should be wellsuited for determining the absolute number of multiple target moleculesin a specified container, for example in high-sensitivity clinicalassays, or for determining the number of transcripts in single cells.The approach should also be compatible with other molecular assaysystems. For example, antibodies could be stochastically labeled withDNA fragments and those that bind antigen harvested. Afteramplification, the number of labels detected will reflect the originalnumber of antigens in solutions. In the examples shown here, DNA is usedbecause of the great diversity of sequences available, and because it iseasily detectable. In principle, any molecular label could be used, forexample fluorescent groups or mass spectroscopy tags, as long as theyare easily detected and they have sufficient diversity for the desiredapplication. Although many of the examples refer to populations

It is instructive to contrast the attributes of stochastic labeling withother quantitative methods. Microarray and sequencing technologies arecommonly used to obtain relative abundance of multiple targets in asample. In the case of microarray analysis, intensity values reflect therelative amount of hybridization bound target and can be used to compareto the intensity of other targets in the sample. In the case ofsequencing, the relative number of times a sequence is found is comparedto the number of times other sequences are found. Although thetechniques differ by using intensity in one case and a digital count inthe other, they both provide relative comparisons of the number ofmolecules in solution. In order to obtain absolute numbers, quantitativecapture of all sequences would need to be assured; however in practicethe efficiency of capture with microarray and sequencing technologies isunknown.

Digital PCR is an absolute counting method where solutions arestochastically partitioned into multi-well containers until there is anaverage probability of one molecule per two containers, then detected byPCR(4). This condition is satisfied when, P₀=(1−e^(−n/c))=½; where n isthe number of molecules and c is the number of containers, or n/c is0.693. Quantitative partitioning is assumed, and the dynamic range isgoverned by the number of containers available for stochasticseparation. Once the molecules are partitioned, high efficiency PCRdetection gives the yes/no answer and absolute counting enabled. To varydynamic range, micro-fabrication can be used to substantially increasethe number of containers (5). Similarly, in stochastic labeling, thesame statistical conditions are met when P₀=(1−e^(−n/m))=½; where m isthe number of labels, and one half of the labels will be used at leastonce when n/m=0.693. The dynamic range is governed by the number oflabels used, and the number of labels can be easily increased to extendthe dynamic range. The number of containers in digital PCR plays thesame role as the number of labels in stochastic labeling and bysubstituting containers for labels we can write identical statisticalequations. Using the principles of physical separation, digital PCRstochastically expands identical molecules into physical space, whereasthe principle governing stochastic labeling is identity based andexpands identical molecules into identity space.

New methods and compositions for single molecule counting employing theuse of stochastic labeling are disclosed herein. In preferred aspects, adiverse set of labels is randomly attached to a population of identicalmolecules is converted into a population of distinct molecules suitablefor threshold detection. Random attachment as used herein refers to aprocess whereby any label can be attached to a given molecule with thesame probability. To demonstrate stochastic labeling methodsexperimentally the absolute and relative number of selected genes weredetermined after stochastically labeling 360,000 different fragments ofthe human genome. The approach does not require the physical separationof molecules and may take advantage of highly parallel methods such asmicroarray and sequencing technologies to simultaneously count absolutenumbers of multiple targets. In some embodiments, stochastic labelingmay be used for determining the absolute number of RNA or DNA moleculeswithin single cells.

The methods disclosed herein may be used to take quantitativemeasurements of copies of identical molecules in a solution bytransformation of the information to a digital process for detecting thepresence of different labels. The stochastic properties of the methodhave been measured, and the relative and absolute digital counting ofnucleic acid molecules is demonstrated. The method is extremelysensitive, quantitative, and can be multiplexed to high levels. In someaspects a microarray-based detection method is used, but the method isextendable to many other detection formats.

In some aspects, the methods are based on probability theory, where theoutcome of chemical reactions occurring between a set of labelingmolecules and a set of target molecules is modeled and tested. When allof the molecules in a uniform mixture of fixed volume collide and reactrandomly, the chemical events follow a stochastic process governed inpart by the molecule concentration of each species (D. T. Gillespie, TheJournal of Physical Chemistry 81, 2340 (1977)).

Methods for analyzing genomic information often utilize a correlationbetween a measurement of the amount of material associated with alocation. The location can be, for example, a feature of an array thatcontains a specific sequence that is known or can be determined or anytype of solid support such as a bead, particle, membrane, etc. A commonaspect to these methods is often hybridization of a target to bemeasured to a complementary probe attached to the solid support. Theprobe may be, for example, an oligonucleotide of known or determinablesequence, but may also be BACs, PACs, or PCR amplicons.

Because of the density of different features that can be obtained usingsynthesis methods such as photolithography, microarrays can be appliedto high density applications. For example, at feature sizes of 1 micronsquare an array can have about 10⁸ features per cm². Within a feature,depending on the chemistry used for synthesis, the probes are spacedtypically at about 10 nm spacing resulting in about 10⁴ molecules in amicron². At approximately full saturation about 10% of those probes arehybridized with target. There are then about 640 functional molecules inan array having 1 micron² spacing between features (˜800 nm² functionalarea). This relatively small number of functional molecules in a featurelimits the dynamic range for estimating relative concentration fromhybridization signal intensity.

Methods are disclosed herein to overcome the dynamic range limitationsobserved with small feature sizes and small numbers of molecules on thearray surface, by using a counting or digital readout as a substitutefor the typical analog signal resulting from array hybridization.

Methods that use signal intensity to estimate relative concentrations oftargets typically label the targets with a detectable label, often afteran amplification step, and through hybridization of the labeled targetto the probe, the probe and thus the feature is also labeled. The amountof label is detected and correlated with a measurement of the amount oftarget in the sample. The estimate of amount of a given target in asample is typically relative to other targets in the sample or topreviously obtained measurements and may be based on comparison totargets present in the sample at known or expected levels or to controlswithin the sample. This type of analysis can and has been usedsuccessfully, for example, to estimate genomic copy number to detectcopy number variation in individuals or in cell populations (see, forexample, Pinkel & Albertson, Annu. Rev. Genomics Hum. Genet. 6, 331-354(2005), Lucito et al. Genome Res. 13, 229102305 (2004), Sebat et al.Science 305, 525-528 (2004), Zhou et al., Nat. Biotechnol. 19, 78-81(2001) and Zhao et al. Cancer Res. 65, 5561-5570 (2005) and US PatentPub. Nos. 20040157243 and 20060035258) or to estimate gene expressionlevels (see, for example, Lockhart et al., Nat. Biotechnol. 14:1675-1680(1996), and Wodicka et al., Nat. Biotechnol. 15:1359-1367 (1997)).

Correlating intensity of hybridization signal or signal intensity withconcentration of target molecules has limitations and can typicallyprovide only an estimate of the absolute amount of a target, and may notbe an accurate count of the actual amount of target present. Theestimate may be an under or over estimate, particularly when comparingdifferent targets or different samples. This is the result of manydifferent factors, including but not limited to, differences betweenprobes, feature specific effects, sample specific effects, feature size(as it decreases the ability to correlate accurately decreases) andexperimental variation. Much of this variation can be addressed by dataanalysis methods, but the methods do not provide counting of individualmolecules or events and are therefore subject to estimation errors.

In preferred aspects methods are disclosed for attaching a differentlabel-tag sequence to each molecule of a particular target sequence ormore preferably a collection of target sequences of interest. Forexample, a sample having 100 molecules of target type 1 is mixed with anexcess, for example, 1000 different label-tag sequences, forming alibrary of label-tag sequences under ligation conditions. Multiplecopies of the library of label-tag sequences are added so there arepreferably many copies of each label-tag. Different label-tag sequencesfrom the library are appended to each of the 100 target molecules sothat each of the 100 molecules of the first target sequence has a uniquelabel-tag sequence appended thereto. This results in 100 differenttarget-label-tag combinations. The target-label-tag molecules may thenbe amplified to enrich the target-label-tag products relative to othernon-targets. Amplification after labeling alters the absolute amount ofthe target, but because each occurrence in the original sample has beenuniquely labeled this will not alter the count. The amplifiedtarget-label-tag products, whether amplified or not, can then be labeledwith a detectable label, and hybridized to an array of probes. Thefeatures of the array that have target-label-tag hybridized thereto canbe detected, for example, by labeling the hybridization complex with afluorescent label and detecting the presence of signal at the features.In this example, because there are 1000 different labels possible and asingle target being analyzed, there are 1000 different possiblelabel-target sequences that might be generated so an array having adifferent feature for each of the 1000 different possibilities can beused. Assuming each target is labeled and no label is used twice, 100 ofthe 1000 different features should be detectable, indicating thecorresponding label has been used.

Consider 1 copy of a target molecule in solution identified as t₁. Reactthis target against a set of 10 labels, L_(m)={l₁, l₂, . . . l₁₀}. Eachlabel has a 0.1 probability of being chosen. Next consider multiplecopies of the target, t_(n), reacted against the set of L_(m) (assumenon-depelting reservoir of labels). For simplicity, consider 3 copies oft: t_(t), t₂ and t₃. Target t₁ will choose a label, t₂ has a 0.9probability of choosing a different label, t₃ has a predictableprobability of choosing the same label as t₁ or t₂. For n copieschoosing from m labels, outcomes can be modeled by the binomialdistribution as discussed above. For 3 targets and 10 labels, theprobability of a label not being chosen, P₀ is (1−( 1/10))³=0.729. Theprobability P₁ of being chosen exactly once is ( 3/10)(1−(1/10))²=0.243. The probability of being chosen twice, P₂ is 0.027 andthe probability P₃ of being chosen 3 times is 0.001. Since P₀ is theprobability of not being chosen, 1−P₀ is the probability of being chosenat least once. We define k=m(1−P₀) as the number of labels we expect tosee in an experiment. Conversely, if we know m, and observe k we cansolve for the number of molecules. In the previous example where n=3 andm=10 we expect to see 10(1−P₀) or 2.71 labels as our most probableoutcome. Increasing m dramatically increases our counting efficiency,accuracy and dynamic range, e.g. for m=1,000, k(number of labelsexpected for n=10, k=9.96, for n=20, k=19.8.

Once the target molecules are labeled with the counter they can beamplified freely without impacting the counting since the readout iseither yes, indicating detection or no indication not detected. In oneaspect, a simple detector having m elements for each target sequence canbe constructed. The detector may be an array. An array having 10⁸features or elements could assay 10⁵ different targets using 10³different labels, for example. Other detection methods do not requireindividual elements for each counter, for example, sequencing.

In preferred aspects the “counter library” or “label-tag library” hasapproximately the same number of copies of each label-tag in thelibrary. The label-tag sequences are not target specific, but are likethe tags that have been used for other tagging applications, forexample, the Affymetrix GENFLEX tag array. Preferably all label-tags ina set of label-tags will have similar hybridization characteristics sothat the label-tags of the set can be detected under similar conditions.

For each target there are a series of features on the array, preferablyone feature for each label-tag. In each of these features the portion ofthe probe that hybridizes to the target (or target complement) is thesame but the label-tag complement is different in each feature. Forexample, to detect a first target RNA, “RNA1”, there would be a seriesof features each having a different probe (RNA1-tag1, RNA1-tag2, . . .RNA1-tagN). For each target to be detected there is a similar set offeatures, e.g. RNA2-tag1, RNA2-tag2, . . . RNA2-tagN. The set oflabel-tags is N tags and it is the unique combination of the label-tagwith the target sequence that creates a novel sequence to be detected,for example, by hybridization.

Label-tag attachment to individual targets is a stochastic processwhereby the probability of any given label-tag being attached to anytarget is stochastic. There is a random selection of label-tags byattaching the label-tags to the end of a known target sequence in asequence independent manner. The label-tag is attached withoutrequirement for it to hybridize to any portion of the target so there isno or minimal bias as to which label-tag sequence is attached.Individual molecules all look the same for the purpose of attachment ofthe label-tag.

The label-tag may be attached to the target by any method available. Inone embodiment, the label-tag is attached by ligation of the label-tagto one of the ends of the target. In preferred aspects the probes of thearray are complementary to a predicted junction between target and labelso it is preferable that the labels are attached to all occurrences of atarget at the same position. This is facilitated if the termini of eachoccurrence of a selected target are the same and are known. In oneaspect, target occurrences are fragmented with a restriction enzyme sothat defined ends of known sequence are formed.

After label-tag attachment in some embodiments the target-label-tagsegment is amplified. Attachment of universal primers to either endfollowed by PCR amplification is one method for amplifying. Theuniversal primers may be added along with the label or at a subsequentligation step.

For RNA targets an RNA ligase, such as T4 RNA ligase may be used. T4 RNAligase 1 catalyses the ligation of a 5′phosphryl-terminated nucleic aciddonor to a 3′hydroxyl-terminated nucleic acid acceptor. Substratesinclude single-stranded RNA and DNA. See, for example, Romaniuk, P. andUhlenbeck, O. (1983) R. Wu, L. Grossman and K. Moldave (Eds.), MethodsEnzymol., 100, pp. 52-56. New York: Academic Press and Moore, M. J. andSharp, P. A. (1992) Science, 256, 992-997. RNA targets may also becircularized and used as template for rolling circle amplification usingan enzyme having reverse transcriptase activity. T4 RNA ligase 1 may beused for circularization of RNA by ligating the ends of the moleculetogether. T4 RNA ligase 1 can also be used to ligated RNA to DNA.

Full-length mRNA can be selected by treating total or poly(A) RNA withcalf intestinal phosphatase (CIP) to remove the 5′phosphate from allmolecules which contain free 5′phosphates (e.g. ribosomal RNA,fragmented mRNA, tRNA and genomic DNA). Full-length mRNAs are notaffected. The RNA can them be treated with tobacco acid pyrophosphatase(TAP) to remove the cap structure from the full-length mRNA leaving a5′-monophosphate. A synthetic RNA adapter can be ligated to the RNApopulation. Only molecules containing a 5′-phosphate, (i.e. theuncapped, full-length mRNAs) will ligate to the adapters. Preferably theadapter has a variable label sequence, and may also have a constantsequence for priming. Preferably, the constant sequence is 5′ of thevariable sequence. In some aspects, the adapter ligated mRNA may then becopied to form a first strand cDNA by, for example, random priming orpriming using oligo dT. The cDNA may subsequently be amplified by, forexample, PCR.

T4 RNA ligase may also be used for ligation of a DNA oligo to singlestranded DNA. See, for example, Troutt et al., (1992) Proc. Natl, Acad.Sci. USA, 89, 9823-9825.

In other aspects, the ligated target-label-tag molecule may be enrichedin the sample relative to other nucleic acids or other molecules. Thisenrichment may be, for example, by preferentially amplifying thetarget-label-tag methods, using for example, a DNA or RNA polymerase, orby degrading non target-label-tag molecules preferentially.

In one aspect, the target-label-tag molecule may be nuclease resistantwhile the unligated target and unligated label molecules may be nucleasesensitive. A nuclease can be added to the sample after ligation so thatligated target-label-tag molecules are not digested but non-ligatedmolecules are digested. For example, the targets may be resistant to a5′exonuclease (but not a 3′exonuclease) while the labels are resistantto a 3′exonuclease but not a 5′exonuclease. Ligating target to labelgenerates a molecule that is resistant to 5′ and 3′exonuclease activity.After ligation the sample may be treated with a 5′exonuclease activity,a 3′exonuclease activity or both 5′ and 3′exonuclease activities. Forexamples of nucleases see Rittie and Perbal, J. Cell Commun. Signal.(2008) 2:25-45, which is incorporated by reference (in particular seeTable 5). Exo VII, for example degrades single stranded DNA from boththe 5′ and 3′ ends so the sample could be treated with Exo VII afterligation to degrade molecules that are not ligation products.

In another aspect amplification may include a rolling circleamplification (RCA) step. See for example, Baner et al. (1998) NAR26:5073, Lizardi et al. (1998) Nat. Genet. 19:225, Fire and Xu, (1995)PNAS 92:4641-5, Zhao et al. Angew Chem Int Ed Engl. 2008; 47:6330-6337and Nilsson et al. (2008), Trends in Biotechnology, 24:83-88. Thetargets may be ligated so that they have a label and a universal priming(UP) sequence attached to the 5′ end of the targets. The UP-label-targetis then ligated to form a circle. A primer complementary to the UP isthen hybridized to the circles and extended using a strand displacingpolymerase. The resulting amplification product contains multiple copiesof the complement of the circle, UP-target-L.

In another aspect, targets may be labeled in a copying step. Forexample, a primer having a 3′ target specific region and a 5′ variablelabel region may be hybridized to the targets, either RNA or DNA, andextended to create a single complimentary copy of the target. Eachextension product will have a different label and the junction betweenthe label and the target specific region is known. The extension may beperformed in the presence of nuclease resistant nucleotides so that theextension product is resistant to nuclease but the unextended primersare not. After extension the reaction is treated with a 3′-5′exonucleaseactivity to digest unextended primer. Exonuclease I, for example,removes nucleotides from single stranded DNA in the 3′ to 5′ directionand Exo III removes nucleotides from the 3′ termini of duplex DNA.Exonuclease T (or RNase T) is a single-stranded RNA or DNA specificnuclease that requires a free 3′ terminus and removes nucleotides in the3′ to 5′ direction. The extension products are then detected byhybridization to probes that are complementary to the primers andinclude the unique label portion and the constant target specificportion. If the target is RNA it can be digested with RNase H afterextension. The extension product may also be amplified beforehybridization.

In some aspects the probability that any two targets are labeled withthe same label may be decreased by using two or more labeling steps. Forexample, a first labeling step where each target has a label selectedfrom a set of labels followed by a second labeling set using the sameset of labels. The first labeling event will be independent of thesecond so the probability that the first and second labeling events willboth be the same in two independent targets is the product of theprobability of two targets having the same label in either step. Ifthere are N possible labels, and the first target is labeled first withlabel N1 and then with label N4, the probability that a second targetwill be labeled also with N1 and then N4 is 1/N². So if there are 100different labels, the probability that two targets will be labeled withthe same label in the first round and the same label in the second roundis 1/10,000.

In another aspect a first round of labeling may be done with 16 probes(for example, all possible 2 base combinations) and then a second roundof labeling is done using the same 16 probes. The chance of any oneprobe attaching to a given target occurrence in the first round is 1 outof 16, the chance that the same probe will attach to the second targetis 1/16 and the chance that the same two probes will attach is 1/16×1/16or 1/256.

In another aspect reversible terminators are used to add a sequence tothe end of each target being counted. For example, a 6 base sequence maybe added and the chance of two being the same is 1 in 4⁶ or 1 in 4096.See, for example, WO 93/06121 and U.S. Pat. No. 6,140,493 which disclosestochastic methods for synthesizing random oligomers.

There is a finite set of labels, L_(1-x) and each target to be detectedis present in the sample at a certain integer occurrence (T1_(1-t) ¹,T2_(1-t) ², . . . TN_(1-t) ^(n)). In a preferred aspect, the method isused to count the number of each of the different targets, (e.g. howmany occurrences of T1, how many of T2, . . . how many of TN) in thesample. The targets are independently labeled with the label molecules.Labeling is stochastic, so that any given target occurrence can belabeled with any one of the labels. For example, T1-1/L689, T1-2/L3,T1-3/L4,567 and so on. For Target 2, any given occurrence can also belabeled with any of the label molecules. This might generate, forexample, (T2-1, L5), (T2-2, L198), (T2-3, L34) and so on. There aremultiple copies of each label so T2-1 might be labeled with L5 andT1-500 may also be labeled with L5.

The methods disclosed herein may be used to measure random cell-to-cellvariations in gene expression within an isogenic population of cells.Such variation can lead to transitions between alternative states forindividual cells. For example, cell-to-cell variation in the expressionof comK in B. subtilis has been shown to select cells for transition tothe competent state in which genes encoding for DNA uptake proteins areexpressed. See, Maamar et al. Science 317:526-529 (2007) which isincorporated herein by reference.

In some aspects the labels are generated within the target to becounted. For example, the label may be a unique cleavage site in atarget fragment as shown in FIG. 6. Each of the copies of the target tobe counted 601 have a common sequence at one end identified in thefigure as 603. This may be a common sequence that has been added to thetargets through ligation or primer extension or it may be a naturallyoccurring sequence in the target. The targets are fragmented randomly,for example by shearing or sonnication resulting in cleavage at thepoints indicated by the arrows to generate cleavage products 604.Cleavage is at a different and unique site in each of the fragments andresults in a unique sequence in the target immediately to the left ofthe point of cleavage in the illustration (indicated by circles infragments 607). This unique sequence can function as a label for thedisclosed methods. A second common sequence 605 may be attached to eachof the targets immediately downstream of the cleavage point, through forexample ligation of an adaptor sequence. The resulting targets 607 canbe analyzed directly to determine how many unique sequences are presentand using this number as an indication of the number of targets in thestarting sample. This is illustrated for nucleic acids, but couldsimilarly be applied to proteins or other contiguous strings of monomersor units that are assembled in a non repeating pattern.

FIG. 7 shows a strategy for selecting probes for target fragments. For adouble stranded fragment there are 4 possible junctions that can betargeted with array probes 3001, 3003, 3005 and 3007. Each of thesejunction regions as shown has a counter region 3011 denoted by N's, afixed sequence 3013 that is defined by the restriction enzyme used forfragmentation and a target specific region 3015. The region 3015 isshown as N's but in preferred aspects it is a known and predictablesequence of the target that is adjacent to the selected restrictionsite. In a preferred aspect, the array probes are complementary to atleast a portion of 3011, a portion of 3015 and all of 3013. For eachtarget sequence-counter combination there are 4 different probes thatcould be included on the array. For example, if the targets are 10 locifrom each of 4 chromosomes and 4 probes per fragment are included for1200 different labels (1000 specific plus 200 non-specific) the arraywould have 192,000 total probes (4×10×4×1200).

In some aspects methods for selecting a collection of labels optimizedfor use in the disclosed methods is contemplated. For example, a list ofall possible 14 mers may be used as a starting pool (4¹⁴ is ˜268 milliondifferent sequences). Different label lengths can be used resulting indifferent numbers of starting sequences. Eliminate all labels that arenot at least 50% GC content. Eliminate all labels that do not use eachof the 4 possible nucleotides at least twice. Eliminate all labels thathave more than two Gs or Cs in tandem, e.g. a probe with GGG or CCCwould be eliminated, or with more than three As or Ts in tandem, e.g.AAAA or TTTT would be removed. Remove labels that contain a selectedrestriction site. Remove labels having a Tm that is outside of the range(38.5 to 39.5° C.). In other embodiments the range may be about 38 to40, 38-39, or 39-40. Remove probes that have self complementarity beyonda selected threshold. Perform a hierarchical clustering to maximizesequence differences between labels to minimize cross hybridization,same label to same probe. Minimize self-complementarity within thecollection to reduce tendency of two labels binding to each other.

FIG. 8 shows a counter adaptor 3101 that includes a counter region 3103,a constant region for priming 3105 and a sticky end 3107 for ligation toan overhang created by restriction digestion, for example with BamHI.After ligation of the adaptors 3101 to the target fragment 3109 thereare two adaptors ligated to the target fragment, one at either end. Itis probable that the counters on the two ends will be different althoughthere is a predictable probability of having the same counter ligated toboth ends of the same fragment. After adaptor ligation the fragment 3111can be amplified by PCR using a common primer to the 3103 region of theadaptor. The adaptor may first be filled in to make it double stranded.The PCR amplification may be used to preferentially amplify fragments ofa selected size range, for example, 300 to 2 kb. Smaller fragments arenot amplified as efficiently because of self complementarity between theends of the individual strands (capable of forming a panhandle structurethat inhibits amplification) and longer fragments (longer than about 3kb) also don't amplify well.

After circularization, the uncircularized fragments can be digestedusing an exonuclease, for example. The circularized fragments can beamplified using target specific primers to generate amplificationproduct 3113. In the figure the target specific primers are identifiedas TS primer F and TS primer R. Whereas the primers used to amplify 3111are common to all adaptor ligated fragments and will amplify allfragments that are in the size range to be amplified using PCR, the TSprimers are specific for selected targets to be analyzed. Theamplification product 3113 has in the 5′ to 3′ direction, targetspecific sequence, overhang sequence, a first counter, first adaptorsequence, circularization junction 3115, second adaptor sequence, secondcounter, second overhang sequence and a second target specific sequence.The first and second counter are different (although they may be thesame at a low probability) and the first and second target sequence aredifferent. The product 3113 or preferably fragments thereof can bedetected by a variety of methods, for example, an array of probes asexemplified by probe 3117 can be used. The array probe 3117 iscomplementary to a region of the target, the overhang region and thecounter. When hybridized the target will have an overhanging singlestranded region that corresponds to the adaptor sequence. A labeledprobe 3119 that is complementary to one strand of the adaptor can behybridized and the ligated to the array probe as shown, and as describedbelow.

FIG. 9 shows a method for reading out the labeled targets on arrays. Onthe left, the target with G₁ ligated to L₁, “G₁L₁”, is shown hybridizingto the complementary array probe over the entire length of the probe. Onthe right target G₁ ligated to label L₂ is shown partially hybridized tothe G₁L₁ probe on the array. On the left the biotin labeled constantsegment can hybridize to the G₁L₁ target and ligate to the 5′ end of theG₁L₁ array probe. The constant segment can hybridize to the L₂ segmentbut will not ligate to L₁. This allows for labeling of properlyhybridized target-label pairs with both hybridization and ligationdiscrimination. The lower panel shows an example where the target or Gportion is not matching with the probe on the array. This will notligate efficiently because it hybridizes less stably.

The left panel shows the results when target G₁ ligated to label L₁ toform G₁L₁ hybridizes to the complementary G₁L₁ probe on the array. Theconstant region (in white) can hybridize to its labeled complement sothat the 3′ end of the labeled complement is juxtaposed with the 5′ endof the L₁ region of the probe on the array and the ends can be ligated.In the center panel the target hybridizing to the G₁L₁ probe isnon-cognate, the label region is L₂ and not L₁ so it does not hybridizeto the L₁ region of the probe. The labeled oligo can hybridize to thepartially hybridized target but it is not juxtaposed with the 5′ end ofthe L₁ region of the probe so it should not ligate to the probe. In theright panel the target shown hybridized has the L₁ region and iscomplementary to the array probe at that region, but the array probe hasa G region that is not G₁ so the G₁L₁ target does not hybridize. Thelabeled oligo can hybridize to the target but because the L1:L1 regionis short the duplex is not stable and the labeled oligo does not ligateto the end of the array probe.

If you have N targets T (T₁, T₂, . . . T_(N)) and each is present at anumber of copies C (C1, C2, . . . C_(x)) where X varies from target totarget (X_(T1), X_(T2), . . . X_(TN)) and you ligate to a set of Ydifferent labels (L₁, L₂, . . . L_(Y)) then you generate, for example,T₁C₁L₁, T₁C₂L₂, . . . T_(N)C_(X)L_(XT1), where X<<<Y). So, for example,if T1 is gene A and T2 is gene B and gene A is present in the sample at500 copies and gene B is present at 100 copies, each copy of gene A, 1to 500, will be attached to a different label (so there will be ˜500different labels attached to the gene A copies), and each copy of geneB, 1 to 100, will be attached to a different label.

A method for counting the number of occurrences of each of a pluralityof same targets in a mixture of targets comprising multiple occurrencesof each type of a plurality of different targets. In preferred aspects,the mixture of targets is a nucleic acid sample that contains differentamounts of multiple target sequences. For example, there may be targetsequences 1, 2, 3, 4 and 5 that are expression products from 5 differentgenes, occur in the sample as follows: 1000 copies of target 1, 100copies of target 2, 500 copies of target 3, 10 copies of target 4 and 50copies of target 5. The targets are preferably of known sequence and aretreated so that they may be ligated to a label-tag sequence.

FIG. 1 shows one embodiment of the method. Labels or counters 101 arecombined with assay targets 103 so that each target is combined with onelabel to form label-targets 105. The process of combining an individualtarget with individual label molecules is a stochastic process. Thenumber of labels each target type combines with is directly proportionalto the number of individual targets of that target type or the copynumber of the target. The number of labels is counted by hybridizationto arrays where individual label-targets are detected at differentfeatures.

The targets are mixed with a collection of label-tag sequences, eachlabel-tag being a different sequence and the collection having a numberthat is preferably 10 times the number of copies of the most abundanttarget to be counted. In a preferred aspect, the label-tags are acollection of known sequences such as a collection of all possibletimers (N₆). Each of the label-tag sequences is present in multiplecopies in the mixture, but all are present at approximately equalamounts. The label-tag sequences are ligated to the targets. Ligation israndom so that any given label-tag has about the same probability ofligating to any one target occurrence. So if there are 1000 differenttargets each could be ligated to a different label-tag sequence and theprobability that any two target occurrences will have the same label-tagligated is low. Because the ligation is a random stochastic processthere is a known probability that if there are C copies of a giventarget and N different label-tags that any two copies of a target T willhave the same label.

T1, T2, . . . TN. C1, C2, . . . CX, L1, L2, . . . LY where T are thedifferent targets and there are N different targets, C are the differentcopies of a target and there are X copies of that target and L are thedifferent label label-tags and there are Y label tags. X varies for eachtarget and determining X is one of the objects of the present invention.The relationship between X and Y determines the probability that two C'swill have the same L. In preferred aspects Y is greater than X for eachtarget to be counted. This reduces the probability of undercounting dueto double labeling. If C1 and C2 of T1 are both labeled with L3 bothcopies will be counted as a single occurrence, resulting in undercounting. Undercounting can also be adjusted for by estimating thenumber of copies that are likely to be multiply labeled and adjustingthe final count upwards to take those into account. For example, ifthere is a likelihood that 5 of 1000 copies will be labeled with thesame label tag then the final number should be adjusted up by 0.5%.

In preferred aspects, the detection is by hybridization to an array ofprobes. The array has a collection of features for each target thatincludes a different feature for each label tag. For example, if thereare X label tags there are X features for each target, T1L1, T1L2, . . .T1LX and the same for target 2, T2L1, T2L2, . . . T2LX, out to TNL1,TNL2, . . . TNLX. The number of features of the array is on the order ofX times N. Each probe has a target complementary sequence and a labeltag complementary sequence. Within a set of probes for a given targetthe target segment of the probe would remain constant and the label tagportion varies from feature to feature so that each label tag sequenceis represented by at least one feature for each target.

In one aspect, the methods may be used to count the number of copies ofeach of a plurality of targets in a sample. The amount of targetcontaining sample mixed with the label tags may be diluted so that thenumber of copies of each target to be counted is less than the number oflabel tags. For example, if the targets to be counted are present atabout 1,000 copies per cell and there are 10,000 label tags you want tohave the amount of sample in the mixture to be about the equivalent ofone cell's worth of RNA. You can mix that with multiple copies of eachlabel-tag, but you want to keep the absolute number of copies of targetbelow the number of types of label tag sequences. Dilution of the sampleand use of an appropriately small amount of starting material may beused. If a target sequence is present at low copy number per cell it ispossible to use the nucleic acid from a larger number of cells. Forexample, to measure the DNA copy number of a chromosomal region relativeto other chromosomal regions the expected copy number is low (e.g. 2 fornormal) so if there are 10,000 different label tags, the number ofgenomes that can be added to the sample for attachment of label tags canbe high, e.g. 500 to 1000.

In one aspect, the methods are used to identify regions of genomicamplification and chromosomal abnormalities. For example, the methodsmay be used to detect trisomy. Most of the chromosomal regions will bepresent in 2 copies per cell and the region of trisomy will be presentin 3 copies per cell. You would expect to observe a 3:2 ratio in yourcount. For example, if you have 500 genomes you would have 1000 copiesof most regions and 1500 copies of the trisomy regions. Small errors inthe counting, resulting from undercounting, would have little or noeffect on the counting.

In some aspects, controls of known copy number may be spiked in to asample to determine accuracy.

Stochastic labeling of t_(1, N) (collection of essential identicalmolecules of copy 1, 2. . . N of target 1) by L_(1,m) (effectively aninfinite reservoir of diversity m when m is much greater than N). Thisallows for complete or near complete resolution of members of t_(1,N),by imparting separate identities to the members of the collection oft_(1,N) (provided that M is sufficiently smaller than N in thelabeling). This provides for a stochastic or random projection oft_(1,N) onto L_(1,m). In some aspects L_(1,m) is a library and themembers of the library that are associated with t_(1,N) can be countedto determine the number of copies of the target. In some aspects themethods can be described as indexing the members of the target. Thisprovides a method to follow individual molecules that are members of atype of molecule that would not otherwise be distinguishable one fromanother.

Because stochastic labeling can impart identifiability to otherwisenon-identifiable molecules it can impart identifiability to any twotargets that may be very similar, but different. Examples of targetsthat may be highly similar but could be separately counted using thedisclosed methods, include, for example, alternative splice forms of agene, and sequences that have one or more variations, including avariation in a single base (e.g. SNP or indels (insertion or deletionsof short regions, e.g. 1-5 bases). In some aspects the methods impart aclonal labeling, that allows a single copy to be separately detected andseparately isolated from the solution.

Some nucleic acid sequencing reactions use methods that stochasticallyattach targets to a solid support followed by amplification of theattached target and analysis. The target attaches in an unknown locationand the location can be determined by sequencing the amplified target atspecific locations. In contrast, the disclosed methods provide forclonal amplification of known targets in a known location. Thestochastic nature of the formation of the target-label-tag moleculeprovides a mechanism for isolating single occurrences of selectedtargets that can be subsequently amplified and analyzed. In some aspectsthe label can be used as a handle for isolating clonal populations oftargets. The labeling step generates an indexed library that has avariety of applications. For example, the indexed library could be usedfor sequencing applications. The method adds distinguishability to anyset of molecules, even molecules that are not distinguishable by othermechanisms because they may share common regions or even been identical.The indexed library can be stored and used multiple times to generatesamples for analysis. Some applications include, for example, genotypingpolymorphisms, studying RNA processing, and selecting clonalrepresentatives to do sequencing.

In some aspects the methods are used to stochastically label apolyclonal antibody population. This may be used to identify differentpolyclonal populations.

The methods may be used to convert an analog readout of hybridizationsignal intensities on arrays into a measurable process that can bescored digitally on the arrays. The method leverages a random processwhere the tagging of assayed molecules is governed by stochasticbehavior. In a random process, the more copies of a given target, thegreater the probability of being tagged with multiple labels. A count ofthe number of incorporated labels for each target can approximate theabundance level of a given target of interest. The ability to countlabels on microarrays would be a clear cost-advantage over the otherexisting techniques.

Serial analysis of gene expression (SAGE) is another method for analysisof gene expression patterns. SAGE relies on short sequence tags (10-14bp) within transcripts as an indicator of the presence of a giventranscript. The tags are separated from the rest of the RNA andcollected. The tags can be linked together to form long serial moleculesthat can be cloned and sequenced. Quantitation of the number of times aparticular tag is observed provides an estimate of the relativeexpression level of the corresponding transcript, relative to othertagged transcripts. See, for example, Velculescu et al. Science 270,484-487 (1995) and Velculescu et al. Cell 88 (1997). Again this methodprovides a relative estimate of the abundance of a transcript and not anactual count of the number of times that transcript appears. Othermethods based on counting and estimating relative abundance have alsobeen described. See, for example, Wang et al. Nat. Rev. Genet. 10, 57-63(2009). Additional methods for digital profiling are disclosed, forexample, in U.S. Patent Pub. 20050250147 and U.S. Pat. No. 7,537,897.

A stochastic counting assay system as described herein can also be asub-system within a much larger bio-analysis system. The bio-analysissystem could include all the aspects of sample preparation prior to, forexample, optical detection, the post processing of data collected in theoptical detection phase and finally decision making based on theseresults. Sample preparation may include steps such as: extraction of thesample from the tested subject (human, animal, plant environment etc.);separation of different parts of the sample to achieve higherconcentration and purity of the molecules under investigation; sampleamplification (e.g. through PCR); attachment of fluorescence tags ormarkers to different parts of the sample; and transfer of the sample ora portion of the sample into a reaction vessel or site on a substrate.The post processing of the collected data may include: normalization;background and noise reduction; and statistical analysis such asaveraging over repeated tests or correlation between different tests.The decision making may include: testing against a predefined set ofrules and comparison to information stored in external data-bases.

The applications and uses of the stochastic labeling and countingmethods and sytems described herein can produce one or more resultuseful to diagnose a disease state of an individual, for example, apatient. In one embodiment, a method of diagnosing a disease comprisesreviewing or analyzing data relating to the presence and/or theconcentration level of a target in a sample. A conclusion based reviewor analysis of the data can be provided to a patient, a health careprovider or a health care manager. In one embodiment the conclusion isbased on the review or analysis of data regarding a disease diagnosis.It is envisioned that in another embodiment that providing a conclusionto a patient, a health care provider or a health care manager includestransmission of the data over a network.

Accordingly, business methods relating to the stochastic labeling andcounting methods and methods related to use thereof as described hereinare provided. One aspect of the invention is a business methodcomprising screening patient test samples for the amount of abiologically active analyte present in the sample to produce dataregarding the analyte, collecting the analyte data, providing theanalyte data to a patient, a health care provider or a health caremanager for making a conclusion based on review or analysis of the dataregarding a disease diagnosis or prognosis or to determine a treatmentregimen. In one embodiment the conclusion is provided to a patient, ahealth care provider or a health care manager includes transmission ofthe data over a network.

Applications for the disclosed methods include diagnosing a cancerouscondition or diagnosing viral, bacterial, and other pathological ornonpathological infections, as described in U.S. Pat. No. 5,800,992.Additional applications of the disclosed methods and systems include,pathogens detection and classification; chemical/biological warfarereal-time detection; chemical concentration control; dangerous substance(e.g., gas, liquid) detection and alarm; sugar and insulin levelsdetection in diabetic patients; pregnancy testing; detection of viraland bacterial infectious diseases (e.g. AIDS, Bird Flu, SARS, West Nilevirus); environmental pollution monitoring (e.g., water, air); andquality control in food processing.

Any available mechanism for detection of the labels may be used. Whilemany of the embodiments discussed above use an array readout form, itwill be obvious to one of skill in the art that other methods forreadout may be used. For example, sequencing may be preferred in someembodiments.

In some aspects the readout is on an array. The array may be a solidsupport having immobilized nucleic acid probes attached to the surfacein an ordered arrangement. The probes may be, for example, synthesizedin situ on the support in known locations using photolithography or theprobes may be spotted onto the support in an array format. As discussedabove, in some embodiments the array includes a probe feature for eachpossible label-target combination. A feature preferably includes manycopies of a single probe sequence. The feature may also have some probesthat are not full length, resulting from truncation of synthesis. Thephoto activation process may not be 100% efficient so some probes areterminated at each step without having subsequent bases added. Thesetruncated probes have the sequence of a portion of the full lengthprobe.

Sequencing readout. After attachment of the labels to the targets in astochastic manner, the targets may be amplified according to any of themethods disclosed herein and the amplification product may be subjectedto any available sequencing method.

A number of alternative sequencing techniques have been developed andmany are available commercially. For a review see, for example, AnsorgeNew Biotechnology 25(4):195-203 (2009), which is incorporated herein byreference. These include the use of microarrays of genetic material thatcan be manipulated so as to permit parallel detection of the ordering ofnucleotides in a multitude of fragments of genetic material.

The arrays typically include many sites formed or disposed on asubstrate. Additional materials, typically single nucleotides or strandsof nucleotides (oligonucleotides) are introduced and permitted orencouraged to bind to the template of genetic material to be sequenced,thereby selectively marking the template in a sequence dependent manner.Sequence information may then be gathered by imaging the sites. Incertain current techniques, for example, each nucleotide type is taggedwith a fluorescent tag or dye that permits analysis of the nucleotideattached at a particular site to be determined by analysis of imagedata.

In another aspect, mass spec analysis may be used to detect the labelsand count the targets. The labels can be distinguishable based on sizeor other property that can be detected. Many of the examples providedherein identify the label based on unique nucleic acid sequence but anydistinguishable label may be used, for example, the pool of labels maybe labels that are differentially detectable based on fluorescenceemission at a unique wavelength.

FIG. 9 shows a method for reading out the labeled targets on arrays. Onthe left, the target with G₁ ligated to L₁, “G₁L₁”, is shown hybridizingto the complementary array probe over the entire length of the probe. Onthe right target G₁ ligated to label L₂ is shown partially hybridized tothe G₁L₁ probe on the array. On the left the biotin labeled constantsegment can hybridize to the G₁L₁ target and ligate to the 5′ end of theG₁L₁ array probe. The constant segment can hybridize to the L₂ segmentbut will not ligate to L₁. This allows for labeling of properlyhybridized target-label pairs with both hybridization and ligationdiscrimination. The lower panel shows an example where the target or Gportion is not matching with the probe on the array. This will notligate efficiently because it hybridizes less stably.

The left panel shows the results when target G₁ ligated to label L₁ toform G₁L₁ hybridizes to the complementary G₁L₁ probe on the array. Theconstant region (in white) can hybridize to its labeled complement sothat the 3′ end of the labeled complement is juxtaposed with the 5′ endof the L₁ region of the probe on the array and the ends can be ligated.In the center panel the target hybridizing to the G₁L₁ probe isnon-cognate, the label region is L₂ and not L₁ so it does not hybridizeto the L₁ region of the probe. The labeled oligo can hybridize to thepartially hybridized target but it is not juxtaposed with the 5′ end ofthe L₁ region of the probe so it should not ligate to the probe. In theright panel the target shown hybridized has the L₁ region and iscomplementary to the array probe at that region, but the array probe hasa G region that is not G₁ so the G₁L₁ target does not hybridize. Thelabeled oligo can hybridize to the target but because the L1:L1 regionis short the duplex is not stable and the labeled oligo does not ligateto the end of the array probe.

The methods are broadly applicable to counting a population of moleculesby performing a stochastic operation on the population to generate astochastic population of identifiable molecules. The targets need not beidentical. For example, the methods may be used to count the absolutenumber of members of a group. In one aspect, a sample having an unknownnumber of copies of a selected nucleic acid target is fragmentedrandomly so that on average each copy of the target has a different endresulting from a distinct fragmentation event. A common adaptor sequencecan be ligated to the end of each fragment and used for amplification ofthe fragments. Each ligation event generates a new molecule having ajunction formed by the end of the random fragment and the adaptorsequence. The new junction can be detected by, for example, sequencingusing a primer complementary to the adaptor or a region of the adaptor.Because the fragmentation was a stochastic process the number ofdifferent ends detected is a count of the number of different startingtarget molecules, assuming one fragment per starting target molecule.

The examples provided herein demonstrate the concept of using astochastic labeling strategy in the high sensitivity detection andcounting of individual DNA molecules. The difficult task of quantifyingsingle nucleic acid molecules is converted into a simple qualitativeassay that leverages the statistics of random probability; and at thesame time, the requirement of single molecule detection sensitivity isachieved with PCR for the robust amplification of single DNA molecules.In some aspects improved methods for amplification will be used. Forexample, linear amplification methods may be used to mitigate therepresentation distortions created by exponential cycling in PCR. Giventhe lack of available techniques for single molecule counting, and theincreasing need for its use, the new concept of stochastic labeling islikely to find numerous applications in the near future.

EXAMPLES

To demonstrate stochastic labeling, we performed an experiment to countsmall numbers of nucleic acid molecules in solution. Genomic DNA from amale individual with Trisomy 21 was used to determine the absolute andrelative number of DNA copies of chromosomes X, 4 and 21, representing1, 2 and 3 target copies of each chromosome, respectively. Genomic DNAisolated from cultured B-Lymphocytes of a male caucasion with Trisomy 21was purchased from The Coriell Institute for Medical Research (Catalog#GM01921). The DNA quantity was determined by PICOGREEN dye (Invitrogen)measurements using the lambda phage DNA provided in the kit as referencestandard. DNA quality was assessed by agarose gel electrophoresis.

The DNA concentration in the stock solution was measured by quantitativestaining with picogreen fluorescent dye, and dilutions containing 3.62ng, 1.45 ng, 0.36 ng and 0.036 ng were prepared. In each dilution, thenumber of copies of target molecules in the sample was calculated from atotal DNA mass of 3.5 pg per haploid nucleus (see, T. R. Gregory et al.,Nucleic Acids Res 35, D332 (2007) , and represent approximately 500,200, 50 and 5 haploid genomes. The absolute quantity of DNA in thesample was determined by optical density measurements and quantitativestaining with PICOGREEN fluorescent dye (Invitrogen) prior to makingdilutions.

As outlined in FIG. 3, the genomic DNA sample 1901 was first digested tocompletion with the BamHI restriction endonuclease to produce 360,679DNA fragments 1905. A diverse set of labels consisting of 96014-nucleotide sequences was synthesized as adaptors harboring BamHIoverhangs (SEQ ID Nos. 44-1963). Genomic DNA was digested to completionwith BamHI (New England BioLabs, NEB) and ligated to a pool of adaptorsconsisting of an equal concentration of 960 distinct labels. Eachadaptor consists of a universal PCR priming site, a 14 nucleotide longcounter sequence and a BamHI overhang (similar to the form of theadaptor shown in FIG. 7). The sequence of the label adaptors SEQ ID Nos.44-1963 were selected from an all-possible 4¹⁴ nucleotide combination tobe of similar melting temperature, minimal self-complementation, andmaximal differences between one-another. Homopolymer runs and thesequence of the BamHI restriction site were avoided. Each pair, forexample, SEQ ID Nos. 44 and 45, form an adaptor pair that has a regionof complementarity starting at base 12 in SEQ ID No. 44 and base 5 inSEQ ID No. 45:

SEQ ID 44 5′ CGACAGACGCCTGATCTTTTGTTAGCCGGAGT 3′ SEQ ID 45 3′ACTAGAAAACAATCGGCCTCACTAG 5′The adaptors have a 5′ overhang of 11 bases in the even numbered SEQ IDsand 4 bases (GATC) in the odd numbered SEQ IDs. Oligonucleotides weresynthesized (Integrated DNA Technologies) and annealed to formdouble-stranded adaptors prior to pooling. For ligation, the digestedDNA was diluted to the desired quantity and added to 100 pmoles(equivalent to 6×10¹³ molecules) of pooled label-adaptors, and 2×10⁶units (equivalent to 1×10¹³ molecules) of T4 DNA ligase (NEB) in a 30 μlreaction. The reaction was incubated at 20° C. for 3 hours untilinactivation at 65° C. for 20 minutes.

For the stochastic labeling reaction, each DNA fragment-end randomlyattaches to a single label by means of enzymatic ligation of compatiblecohesive DNA ends to generate labeled fragments 1907. High couplingefficiency is achieved through incubation with a large molar excess oflabels and DNA ligase enzyme (˜10¹³ molecules each). At this stage, thelabeling process is complete, and the samples can be amplified asdesired for detection. A universal primer may be added added, and theentire population of labeled DNA fragments may be PCR amplified. The PCRreaction preferentially amplifies approximately 80,000 fragments in the150 bp-2 kb size range (FIG. 21). Adaptor-ligated fragments wereamplified in a 50 μl reaction containing 1× TITANIUM Taq PCR buffer(Clontech), 1M betaine (Sigma-Aldrich), 0.3 mM dNTPs, 4 μM PCR004StuAprimer (SEQ ID No. 1974), 2.5 U Taq DNA Polymerase (USB), and 1×TITANIUM Taq DNA polymerase (Clontech). An initial PCR extension wasperformed with 5 minutes at 72° C.; 3 minutes at 94° C.; followed by 5cycles of 94° C. for 30 seconds, 45° C. for 45 seconds and 68° C. for 15seconds. This was followed by 25 cycles of 94° C. for 30 seconds, 60° C.for 45 seconds and 68° C. for 15 seconds and a final extension step of 7minutes at 68° C. PCR products were assessed with agarose gelelectrophoresis and purified using the QIAQUICK PCR purification kit(Qiagen).

The purified PCR product was denatured at 95° C. for 3 minutes prior tophosphorylation with T4 polynucleotide kinase (NEB). The phosphorylatedDNA was ethanol precipitated and circularized using the CIRCLIGASE IIssDNA Ligase Kit (Epicentre). Circularization was performed at 60° C.for 2 hours followed by 80° C. inactivation for 10 minutes in a 40 μlreaction consisting of 1× CIRCLIGASE II reaction buffer, 2.5 mM MnCl₂,1M betaine, and 200 U CIRCLIGASE II ssDNA ligase. Uncirculated DNAs wereremoved by treatment with 20 U Exonuclease I (Epicentre) at 37° C. for30 minutes. Remaining DNA was purified with ethanol precipitation andquantified with OD₂₆₀ measurement.

Amplification of gene targets. Three assay regions were tested: One oneach of chromosomes 4, 21 and X. The genomic location (fragment startingand ending positions are provided), of the selected fragments are asfollows: Chr4 106415806_106416680 (SEQ ID No. 1), Chr2138298439_38299372 (SEQ ID No. 2), and ChrX 133694723_133695365 (SEQ IDNo. 3). The lengths are 875, 934 and 643 bases respectively. Thecircularized DNA was amplified with gene specific primers (SEQ ID Nos.4-9) in a multiplex inverse PCR reaction. PCR primers were picked usingPrimer3 (available from the FRODO web site hosted by MIT) to yieldamplicons ranging between 121 and 168 bp. PCR was carried out with 1×TITANIUM Taq PCR buffer (Clontech), 0.3 mM dNTPs, 0.4 μM each primer, 1×TITANIUM Taq DNA Polymerase (Clontech), and ˜200 ng of the circularizedDNA. After denaturation at 94° C. for 2 minutes, reactions were cycled30 times as follows: 94° C. for 20 seconds, 60° C. for 20 seconds, and68° C. for 20 seconds, with a 68° C. final hold for 4 minutes. PCRproducts were assessed on a 4-20% gradient polyacrylamide gel(Invitrogen) and precipitated with ethanol.

The amplified DNA was fragmented with DNase I, end-labeled with Biotin,and hybridized to a whole-genome tiling array which spans the entirenon-repetitive portion of the genome with uniform coverage at an averageprobe spacing of ˜200 nt (see Matsuzaki et al., Genome Biol 10, R125(2009) and Wagner et al. Systematic Biology 43, 250(1994)). Probeintensity (“Array Intensity”) from the whole-genome tiling array(y-axis) is grouped into 200 nt bins by the length of the BamHI fragmenton which it resides. High probe intensity demonstrates the amplificationof fragments in the 600 bp ˜1.2 kb size range (x-axis, log-scale). Thecomputed size distribution of BamHI restricted fragments in thereference genome sequence (NCBI Build 36) is shown by the curve labeled“Number of Fragments”. After circularization of the amplified productsto obtain circles 1909, three test target fragments were isolated usinggene-specific PCR; one on each of chromosomes X, 4, and 21, and preparedfor detection.

The three labeled targets were counted using two sampling techniques:DNA microarrays and next-generation sequencing. For the array counting,a custom DNA array detector capable of distinguishing the set of labelsbound to the targets was constructed by dedicating one array element foreach of the 960 target-label combinations. Each array element consistsof a complementary target sequence adjacent to one of the complements ofthe 960 label sequences (as shown in FIG. 3).

Array Design: For each gene target assayed, the array probes tiledconsist of all possible combinations of the 960 counter sequencesconnected to the two BamHI genomic fragment ends (FIG. 8). An additional192 counter sequences that were not included in the adaptor pool werealso tiled to serve as non-specific controls. This tiling strategyenables counter detection separately at each paired end, since eachtarget fragment is ligated to two independent counters (one on eitherend).

Arrays were synthesized following standard Affymetrix GENECHIPmanufacturing methods utilizing lithography and phosphoramiditenucleoside monomers bearing photolabile 5′-protecting groups. Arrayprobes were synthesized with 5′ phosphate ends to allow for ligation.Fused-silica wafer substrates were prepared by standard methods withtrialkoxy aminosilane as previously described in Fodor et al., Science251:767 (1991). After the final lithographic exposure step, the waferwas de-protected in an ethanolic amine solution for a total of 8 hrsprior to dicing and packaging.

Hybridization to Arrays: PCR products were digested with Stu I (NEB),and treated with Lambda exonuclease (USB). 5 μg of the digested DNA washybridized to a GeneChip array in 112.5 μl of hybridization solutioncontaining 80 μg denatured Herring sperm DNA (Promega), 25% formamide,2.5 pM biotin-labeled gridding oligo, and 70 μl hybridization buffer(4.8M TMACl, 15 mM Tris pH 8, and 0.015% Triton X-100). Hybridizationswere carried out in ovens for 16 hours at 50° C. with rotation at 30rpm. Following hybridization, arrays were washed in 0.2×SSPE containing0.005% Trition X-100 for 30 minutes at 37° C., and with TE (10 mM Tris,1 mM EDTA, pH 8) for 15 minutes at 37° C. A short biotin-labeledoligonucleotide (see 3119 in FIG. 8) was annealed to the hybridizedDNAs, and ligated to the array probes with E.coli DNA ligase (USB).Excess unligated oligonucleotides were removed with TE wash for 10minutes at 50° C. The arrays were stained with Streptavidin,R-phycoerythrin conjugate (Invitrogen) and scanned on the GCS3000instrument (Affymetrix).

In order to maximize the specificity of target-label hybridization andscoring, we employed a ligation labeling procedure on the capturedsequences (FIG. 8). We set thresholds to best separate the intensitydata from the array into two clusters, one of low intensity and one ofhigh intensity to classify labels as either being used or not (FIGS. 22,23 and 29). We score a label as “present” and counted if its signalintensity exceeded the threshold. To count labels we set thresholds forthe array intensity, or the number of sequencing reads. Appropriatethresholds were straightforward to determine when used and un-usedlabels fall into two distinct clusters separated by a significant gap.In situations where a gap was not obvious, the function normalmixEM inthe R package mixtools was used to classify labels. This function usesthe Expectation Maximization (EM) algorithm to fit the data by mixturesof two normal distributions iteratively. The two normal distributionscorrespond to the two clusters to be identified. The cluster of labelswith a high value is counted as “used”, and the other as “not used”. Theaverage of the minimum and maximum of the two clusters,(I_(min)+I_(max))/2, was applied as the threshold for separating the twoclusters.

Sampling error calculation. A sampling error can be introduced whenpreparing dilutions of the stock DNA solution. This error is a directconsequence of random fluctuations in the number of molecules in thevolume of solution sampled. For example, when exactly 10 μl of a 100 μlsolution containing 100 molecules is measured, the actual number ofmolecules in the sampled aliquot may not be exactly 10. The lower theconcentration of the molecules in the entire solution, the higher thesampling error, and the more likely the actual abundance in the sampledaliquot will deviate from the expected abundance (n=10). To calculatesampling errors, we determined the number of molecules for eachchromosome target in our stock DNA solution and performed numericalsimulations to follow our dilution steps in preparing the test samples(3.62 ng, 1.45 ng, 0.36 ng and 0.036 ng). To illustrate, if the dilutionstep is sampling 1 μl of a 25 μl solution containing 250 molecules, wecreate 25 bins and randomly assign each of the 250 molecules into one ofthe bins. We randomly choose one bin and count the number of moleculesassigned to that bin to simulate the process of sampling 1/25^(th) ofthe entire solution. If a serial dilution was performed, we would repeatthe simulation process accordingly. For each dilution, the observed copynumber ratios of Chr 4:X or 21:X for 10,000 independent trials aresummarized as observed medians, along with the 10^(th) and 90^(th)percentiles and shown in FIGS. 12 and 13.

As an alternate form of detection, the samples were submitted to twoindependent DNA sequencing runs (FIG. 10). The arrangement and positionof the adaptors and PCR primers used to convert the DNA samplehybridized to microarrays into sequencing templates are shown in thefigure. The circularized junction 3115 is located between the twocounter labels. PCR primers that have restriction sites are used toamplify two fragments. The fragments are digested with the restrictionenzymes to generate ends compatible with ligation to sequencingadaptors. The sequencing adaptors are ligated to the ends to generate afragment that has the label sequence and a portion of the target that is48 to 94 base pairs in length are flanked by sequences for use withSOLID sequencing.

Validation by DNA sequencing (First SOLID run). DNA targets that wereused for hybridization to arrays were converted to libraries forsequencing on the SOLID instrument (ABI). P1 and P2 SOLID amplificationprimers were added to the DNA ends through adaptor ligation and strandextension from gene-specific primers flanked by P1 or P2 sequences (FIG.10). Each sample received a unique ligation adaptor harboring a 4-baseencoder (SEQ ID Nos. 34-43) that unambiguously identifies theoriginating sample of any resulting read. Each adaptor includes twostrands, SEQ ID Nos. 34 and 35, 36 and 37, 38 and 39, 40 and 41 or 42and 43, that hybridize to form a double stranded region of 29 base pairsand a single stranded 4 base overhang (GATC). Individual libraries wereprepared for each sample, and quantified with picogreen before equalamounts of each sample was combined into a single pooled library. DNAsequencing was performed on SOLID v3 by Cofactor Genomics. A total of˜46 million 50 base reads were generated. Each read is composed of threesegments, corresponding to the sample encoder, label sequence and genefragment (FIG. 10). We removed reads if: uncalled color bases werepresent, the average Quality Value (aQV) of the whole read <10, the aQVof the sample encoder <20, or the aQV of the label sequence <18. 40% ofthe raw reads were removed. Filtered reads were mapped to referencesequences using the program Short Oligonucleotide Color Space (SOCS),available from ABI with a maximum tolerance of 4 color mismatchesbetween the first 45 color bases in each read and reference sequences(the last 5 color bases on 3′ end of each read were trimmed inalignment). About 64.3% reads were uniquely mapped to referencesequences, of which 89.5% (16 million) have high mapping quality, i.e.,with no mismatch in the sample encoder and at most 1 mismatch in thelabel sequence. These high-quality reads, accounting for ˜35% of thetotal reads generated, were used in subsequent counting analysis.

Sequencing replication (Second SOLID run). An aliquot of the exact sameDNA library originally sequenced by Cofactor Genomics was subsequentlyre-sequenced by Beckman Coulter Genomics. Approximately 50 million 35base reads were generated, and processed following the same rules.Approximately 61% of the raw reads passed quality filters, of which 81%uniquely mapped to a reference sequence with a maximum tolerance of 3color mismatches (An adjusted mismatch tolerance was applied in thealignment step to account for the shorter length of these reads). Of themapped reads, 91% (22.5 million) are of high mapping quality, i.e., withperfect match in the sample encoder and at most 1 mismatch in the labelsequence. These high-quality reads (45% of the total raw readsgenerated) were used for counting analysis.

Between several hundred thousand to several million reads were used toscore the captured labels. Table 1 shows the number of mapped reads fromSOLID DNA sequencing.

TABLE 1 DNA sample 5 ng 2 ng 0.5 ng 0.05 ng 0 ng Chr4 Left side 1^(st)SOLiD run 709,076 252,211 237,380 316,629 1,204 2^(nd) SOLiD run 621,37273,962 189,937 237,520 411 Right side 1^(st) SOLiD run 1,724,9551,662,958 1,114,246 2,201,078 3,353 2^(nd) SOLiD run 1,422,673 1,359,512839,775 980,616 2,386 Chr21 Left side 1^(st) SOLiD run 1,615,4161,474,208 832,234 1,428,540 1,851 2^(nd) SOLiD run 1,296,685 1,038,456622,429 930,461 840 Right side 1^(st) SOLiD run 1,124,772 886,421551,192 849,204 821 2^(nd) SOLiD run 910,298 522,358 367,207 479,621 224ChrX Left side 1^(st) SOLiD run 444,960 316,975 254,386 515,213 7442^(nd) SOLiD run 266,606 157,860 137,706 220,121 5 Right side 1^(st)SOLiD run 1,227,047 921,214 777,033 1,064,531 64 2^(nd) SOLiD run1,043,475 768,296 559,038 695,873 43

We set thresholds for the number of sequencing reads observed for eachlabel, and score a label as “present” and counted if the number ofsequencing reads exceeded the threshold. Label usage summaries fromexperimental observations or from the stochastic modeling are shown inTable 2. The number of attached labels, k, detected for each target ineach dilution either by microarray counting or sequence counting ispresented in Table 2, and plotted in FIGS. 4 and 5.

Several dilutions (3.62 ng, 1.45 ng, 0.36 ng and 0.036 ng) of DNAisolated from cultured of a Trisomy 21 male individual were processedfor microarray hybridization (FIG. 12 left) and DNA sequencing (FIG. 12right). Three gene targets were tested from chromosome X, 4 and 21, andobserved numbers of detected labels are shown (“observed”). The numberof target molecules for each sample was determined from the amount ofDNA used, assuming a single haploid nucleus corresponds to 3.5 pg. Forcomparison, the calculated number of labels expected to appear using astochastic model are also plotted (“calculated”). Numerical values areprovided in Table 4. Relative copy ratios of the three gene targets(FIG. 13): ChrX (right bar), Chr4 (left bar) and Chr21 (center bar)representing one, two and three copies per cell, respectively. Differentdilutions (3.62 ng, 1.45 ng, 0.36 ng and 0.036 ng) of the DNA isolatedfrom cultured lymphoblasts of a Trisomy 21 male individual wereprocessed for microarray hybridization and DNA sequencing. Thecalculated number of target molecules was determined from the number oflabels detected on microarrays (Table 4, column 9) or from the SOLiDsequencing data. For each sample dilution, the copy number ratio of eachgene target relative to ChrX is shown for Microarray (FIG. 13 left) andSOLiD sequencing (FIG. 13 right). For comparison, relative copy ratiosobtained from in silico sampling simulations are also shown in (FIG. 13left) and (FIG. 13 right), where circles indicate the median values from10,000 independent trials and error bars indicate the 10^(th) and90^(th) percentiles. The 90^(th) percentile values of the relative copyratios at the lowest concentration (0.036 ng) are explicitly labeled inthe plots.

TABLE 2 DNA sample 3.62 ng 1.45 ng 0.36 ng 0.036 ng 0 ng Chr4 StochasticModel 633 336 98 10 0 Left side Microarray 501 260 102 14 0 1^(st) SOLiDrun 513 251 101 14 0 2^(nd) SOLiD run 516 273 102 14 0 Right Array 525256 107 14 0 side 1^(st) SOLiD run 544 291 103 13 1 2^(nd) SOLiD run 557307 103 13 1 Chr21 Stochastic Model 769 457 143 15 0 Left sideMicroarray 651 335 160 20 0 1^(st) SOLiD run 678 381 152 20 0 2^(nd)SOLiD run 665 358 161 18 0 Right Microarray 627 341 157 20 0 side 1^(st)SOLiD run 650 381 146 19 0 2^(nd) SOLiD run 653 379 146 19 0 ChrXStochastic Model 400 186 50 5 0 Left side Microarray 281 148 50 11 01^(st) SOLiD run 290 149 43 11 0 2^(nd) SOLiD run 300 150 45 11 0 RightMicroarray 306 133 48 10 1 side 1^(st) SOLiD run 336 153 50 12 0 2^(nd)SOLiD run 344 167 43 11 0

The counting results span a range of approximately 1,500 to 5 molecules,and it is useful to consider the results in two counting regimes, belowand above 200 molecules. There is a striking agreement between theexperimentally observed number of molecules and that expected fromdilution in the first regime where the ratio of molecules to labels(n/m) <0.2 (Table 2). Below 200 molecules the data are in tightagreement, including the data from the lowest number of molecules, 5, 10and 15 where the counting results are all within the expected samplingerror for the experiment (The sampling error for 10 molecules isestimated to be 10±6.4, where 10 and 6.4 are the mean and two standarddeviations from 10,000 independent simulation trials).

In the second regime above 200 molecules, there is an approximate 10-25%undercounting of molecules, increasing as the number of moleculesincreases. We attribute this deviation to be due to a distortion in theamplification reaction. PCR-introduced distortion occurs from smallamounts of any complex template due to the differences in amplificationefficiency between individual templates (2, 3). In the present case,stochastic labeling will produce only one (at low n/m ratios), andincreasingly several copies (at higher n/m ratios) of each template.Modeling suggests that simple random dropout of sequences (PCRefficiencies under 100%) generate significant distortion in the finalnumbers of each molecule after amplification. At any labeling ratio,random dropout of sequences due to PCR efficiency will result in anundercount of the original number of molecules. At high n/m ratios, thenumber of labels residing on multiple targets will increase and have astatistical survival advantage through the PCR reaction causing greaterdistortion. In support of this argument, we observe a wide range ofintensities on the microarray and a wide range in the number ofoccurrences of specific sequences in the sequencing experiments (FIGS.23, 29). This effect can be reduced by carrying out the reaction at n/mratios near or less than 0.2, increasing the number of labels m, furtheroptimization of the amplification reaction, or by employing a linearamplification method. Other factors, such as errors from inaccuratepipetting, could also contribute.

The lymphoblast cell line used in this study provides an internalcontrol for the relative measurement of copy number for genes residingon chromosomes X, 4 and 21. FIG. 13 presents the relative number ofmolecules from all three chromosomes normalized to copy number 1 for theX chromosome. As shown, the measurements above 50 molecules all yieldhighly precise relative copy number values. At low numbers of molecules(0.036 ng), uncertainty results because the stochastic variation ofmolecules captured by sampling an aliquot for dilution are significant.Numerical simulations were performed to estimate the sampling variation,and summarized medians, along with the 10^(th) and 90^(th) percentilesof the copy number ratios and are shown in FIGS. 12 and 13 as circlesand range bars, respectively. At the most extreme dilutions, where ˜5,10, and 15 molecules are expected for the chromosome X, 4 and 21 genes,the copy number ratios fall within the expected sampling error.

Overall, the identity of labels detected on the microarrays and insequencing are in good agreement, with only a small subset of labelsunique to each process (Table 7). Despite a high sequencing samplingdepth (Table 1), a small number of labels with high microarray intensityappear to be missing or under-represented in the sequencing results. Incontrast, labels that appear in high numbers in the sequencing reactionalways correlate with high microarray intensities. No trivialexplanation could be found for the labels that are missing from anygiven sequencing experiment. While under-represented in someexperiments, the same labels appear as present with high sequence countsin other experiments, suggesting that the sequences are compatible withthe sequencing reactions.

PCR validation. We used PCR as an independent method to investigateisolated cases of disagreement, and demonstrated that the labels werepresent in the samples used for the sequencing runs.

PCR was used to detect the presence of 16 label sequences (Table 3)which were either observed as high or low hybridization intensity onmicroarrays, and observed with either high or low numbers of mappedreads in SOLID sequencing. The Chr4 gene target was PCR amplified with 3dilutions (0.1 pg, 1 pg, and 10 pg) of the 3.62 ng NA01921 sample, usingthe DNA target that was hybridized to microarrays, or the prepared SOLIDlibrary template. PCR products were resolved on 4% agarose gels andfluorescent DNA bands were detected after ethidium bromide staining

TABLE 3 Micro- 1st 2nd Micro- array SOLiD Label SOLiD SOLiD array targetlibrary ID Label Sequence reads reads intensity template template 112AGATCTTGTGTCCG     0     2 15,907  1   2  182 ATCTTCGACACTGG     0     110,304  3   4  779 TCGAGATGGTGTTC     0     4  9,411  5   6  782TCGGATAGAGAGCA     0     0  6,716  7   8  783 TCGGTACCAACAAC     1     413,132  9  10  290 CCAAGGTTTGGTGA     1    17 10,777 11  12  780TCGCAAGAGGTAAG     1     1  8,915 13  14  570 GGAGTTACGGCTTT     1     2 8,252 15  16  741 TCAACCAGTAAGCC   794   400    466 17* 18* 424CTGTAAACAACGCC 1,191 1,292    527 19* 20* 242 CACGATAGTTTGCC   905   781 1,103 21* 22  859 TGTACTAACACGCC   920   892  1,107 23* 24*  83ACGCTAACTCCTTG 8,629 7,704 19,500 25  26  383 CGTTTACGATGTGG 7,278 6,40219,022 27  28  804 TCTTAGGAAACGCC     0     0     70 29* 30* 834TGCAATAGACGACC     0     1     72 31* 32*

Table 3. PCR detection for the presence of label sequences in theprocessed DNA sample that was hybridized to microarray, or in the DNAsequencing library. Each PCR contained 0.1 pg of template, whichrepresents approximately 1×10⁶ DNA molecules. The number of mappedsequencing reads and the microarray intensity of each of the 16 labelsfor this selected gene target (Chr4, 3.62 ng) are listed. The last 2columns show the gel lane number containing the indicated sample. Thosenumbers indicated by an * correspond to reactions where PCR failed todetect the label sequence in the sample.

Although we can clearly confirm their presence in the sequencinglibraries, it is unclear as to why these labels are missing orunder-represented in the final sequencing data.

To test the stochastic behavior of label selection, we pooled theresults of multiple reactions at low target concentrations (0.36 and0.036 ng), where the probability that a label will be chosen more thanonce is small.

FIG. 14 shows that the number of times each label is used closelyfollows modeling for 1,064 data points obtained from microarraycounting. The graph is a comparison between experimentally observedlabel usage rates (microarray results) with those predicted fromstochastic model (stochastic model). At low target molecule numbers, thechance of multiple target ligations to the same label sequence is low.It is therefore reasonable to consider data from experiments with lowtarget numbers (0.036 ng and 0.36 ng of DNA), from those experiments, atotal of 1,064 labels were observed, with the total frequency of labelusage ranging from 0 to 6. The theoretically expected label usagefrequency for 1,064 target molecules was obtained by performing 5000simulation runs, with multiple independent reactions simulated in eachrun. The error bars indicate one standard deviation from thecorresponding means.

Furthermore, since each end of a target sequence chooses a labelindependently, we can compare the likely hood of the same labeloccurring on both ends of a target at high copy numbers. Table 4 columns10-11 present the experimentally observed frequency of labels occurringin common across both ends of a target and their expected frequency fromnumerical simulations. No evidence of non-stochastic behavior wasobserved in this data.

TABLE 4 # of Expected # Microarray Estimated Expected Expected #molecules of labels in observed # Genomic # of # of of labels inMicroarray inferred from common of labels in DNA molecules labels atcommon observed # microarray across common Gene amount at either eitheracross of labels observed # paired- across target (ng) end endpaired-ends L R Avg of labels ends paired-ends Chr4 3.62 1034 633 417.68± 11.35  501 525 513 733 273.96 ± 10.24  303 1.45 414 336 117.92 ± 7.83 260 256 258 300 69.22 ± 6.43  63 0.36 103 98 9.93 ± 2.81 102 107 104 11011.26 ± 2.99  20 0.036 10 10 0.11 ± 0.32 14 14 14 14 0.20 ± 0.44 0 0 0 00 0 0 0 0 0 0 Chr21 3.62 1551 769 616.74 ± 11.94  651 627 639 1051425.28 ± 11.37  453 1.45 620 457 217.36 ± 9.51  335 341 338 416 118.79 ±7.83  130 0.36 155 143 21.37 ± 3.98  160 157 158 172 25.86 ± 4.38  320.036 15 15 0.24 ± 0.48 20 20 20 20 0.40 ± 0.62 0 0 0 0 0 0 0 0 0 0 0ChrX 3.62 517 400 166.63 ± 8.81  281 306 294 351 90.14 ± 7.08  103 1.45207 186 36.26 ± 4.98  148 133 140 151 20.34 ± 3.94  23 0.36 51 50 2.58 ±1.52 50 48 49 50 2.45 ± 1.51 4 0.036 5 5 0.03 ± 0.16 11 10 10 10 0.10 ±0.31 2 0 0 0 0 0 1 0 0 0 0 1 2 3 4 5 6 7 8 9 10  11Labels detected on microarray experiments are quantified in Table 4.Indicated quantities (col. 2) of genomic DNA derived from a Trisomy 21male sample were tested on 3 chromosome targets (col. 1). The estimatednumber of copies of target molecules (or haploid genome equivalents,col. 3), the number of labels expected by the stochastic model (col. 4),and the actual number of labels detected on microarrays (col. 6-8) aresummarized. Because each gene target fragment paired-end consists ofrandom, independent label ligation events at the left (L) and the right(R) termini, the number of identical labels expected (col. 5) can bepredicted from computer simulations, and compared to the number actuallydetected (col. 11). Given the number of labels detected (col. 8), weobtain the corresponding number of copies of target molecules (col. 9)in our stochastic model, and the predicted occurrences of identicallabels across paired-ends (col. 10). The numbers in col. 5 and 10 arethe means from 5,000 independent simulation runs along with one standarddeviation of the corresponding means, given the number of labels ateither end (col. 4 and col. 9).

The detailed column information for Table 4 is as follows: column 1:name of tested gene targets; column 2: estimated number of targetmolecules at either left or right end, this number is determined byPICOGREEN dye measurement (Molecular Probes, Inc.), the DNAconcentration is also listed in this column; column 3: number of labelsexpected to be observed/used at either end (predicted by theoreticalmodels), given the estimated number of target molecules in 2nd column;column 4: number of labels expected to be observed in common across thepaired-ends (predicted by theoretical models), given the estimatednumber of target molecules in 2nd column; column 5: empirically observednumber of labels used at the left end of gene target; column 6:empirically observed number of labels used at the right end of genetarget; column 7: empirically observed number of labels used in commonacross the paired-ends; column 8: number of target molecules predictedby theoretical models, based on the empirically observed number oflabels used (i.e., number in 7th column); column 9: number of labelsexpected to be observed in common across the paired-ends, given thenumber of target molecules in 8th column; column 10: empiricallyobserved number of labels that were used in common across thepaired-ends of the gene target.

Example X: An array was designed having 48 target sequences. Each targetwas paired with one of 3840 labels or “counters” for a total of 48×3840or 184,320 probes. The probes were 30 mers (30 nucleotides in length)and the assay was designed to test whether or not the 30 mer impartssufficient discrimination. Of the 30 bases, 15 bases are from the labelsand the other 15 bases are derived from the targets. The probes wereassayed to determine if each label-target combination hybridizesspecifically. A phage RNA ligase was used to join labels with targets.Universal priming sites of 18 bases were included on the 5′ end of thelabels and the 3′ end of the targets, facilitating PCR amplification ofthe joined label-targets. The method is diagramed in FIG. 3.

The 3840 distinct label oligos (counters) were single stranded oligospooled from the Ddel TACL primer panel (40 primer plates by 96 wells perplate for 3840 different oligos). An example label oligo 301 is shown

(SEQ ID NO: 1964) 5′ TCGATGGTTTGGCGCGCCGGTAGTTTGAACCATCCAT-3′.The 48 different primers used as “targets” were synthesized using astarget 48 different 21 nucleotide sequences from the Affymetrix TrueTag5K_A array. An example target oligo 307 is shown

(SEQ ID NO: 1965) 5′ GCCATTTACAAACTAGGTATTAATCGATCCTGCATGCC-3′.

The “label” or “counter” oligo has an 18 nt common sequence at the 5′end and a 15-28 nt “label” (or “counter”) sequence at the 3′ end. Anexample “label” 305 is shown. The universal primer 303 common to all ora group of the label oligos has sequence 5′ TCGATGGTTTGGCGCGCC-3′ (SEQID NO: 1966) at the 5′ end and each target oligonucleotide has commonsequence 311 5′ AATCGATCCTGCATGCCA-3′ (SEQ ID NO: 1967) at the 3′ end asuniversal priming sequence. The target oligos vary in sequence at the 5′ends 309.

A 1:1 dilution of each of the 3840 counters was mixed with variousdilutions of each of the 48 target oligos to simulate differentexpression levels under ligation conditions so that the 5′ end of thetarget oligos can be ligated to the 3′ end of the label oligos. Inpreferred aspects T4 RNA ligase may be used to join the ends of thesingle stranded oligos. The 5′ and 3′ ends of the target oligos arephosphorylated and the 5′ and 3′ ends of the label oligos arehydroxylated. After the ligation the products are amplified by PCR usingprimers to the universal priming sequences. Only those fragments thathave both universal priming sequences 303 and 311 will amplifyefficiently.

Each of the 48 target sequences may be tiled with each of the 3,840counters, resulting in a total number of features onarray=48×3,840=184,320. This is the number of different possiblecombinations of target with label. The product of the ligation andamplification reactions is hybridized to the array. For each target, thenumber of features that light up is determined and can be compared tothe known copy number of each target in the input sample.

To test the digital counting methods, also referred to as stochasticlabeling a collection of label-tag sequences was provided. Each has acommon 5′ universal priming sequence, preferably 15-20 bases in lengthto facilitate amplification, and a 3′ label sequence, preferably 17-21bases in length. Each type of primer in the collection has the sameuniversal priming sequence but each type has a label sequence that isdifferent from all of the other types in the collection. In one aspectthere are about 4,000 to 5,000 different types of label sequences in thecollection to be used. For testing the method, a set of 50 targetsequences was synthesized. The target sequences each have a universalpriming sequence at the 3′ end (5′GCTAGGGCTAATATC-3′SEQ ID NO: 1968, wasused in this experiment). Each of the 50 oligo target sequences thatwere generated has a different 21 base sequence from the GENFLEX arraycollection of sequences, for example, 5′ GCCATTTACAAACTAGGTATT'3′ SEQ IDNO: 1970. The collection of label-tag oligos and the collection oftarget oligos was mixed. Various dilutions of the different targets wereused in the mixture of targets to simulate a mixed population present atdifferent levels, for example, different expression or copy numberlevels. T4 RNA ligase was added to ligate the label-tag oligos to thetarget oligos. There are 5000 different types of label oligos and 50different types of target oligos so the majority of the target oligos ofthe same type will be labeled with a type of label oligo that isdifferent from all of the other target oligos of that type. So targetoligo type 1, occurrence 1 will be labeled with a label oligo type A(11A) and target oligo type 1, occurrence 2, will be labeled with adifferent label oligo, label oligo type B (12B). There is a finite andcalculable probability that two or more occurrences of the same targettype will be labeled with the same label oligo (11A and 12A), but thatprobability decreases as the number of different types of label oligosincreases relative to the number of occurrences of any given type oftarget.

The ligated target/label oligos are then amplified using primers to theuniversal priming sites. Labels can be incorporated duringamplification. The labeled amplification product is then hybridized toan array. For each different possible combination of target (50) andlabel (5000) there is a different probe on the array that targets thatjunction of the target ligated to the label. There will therefore be50×5000 different probes on the array or 250,000 different probes.

Scanned images of the 48×3840 array were analyzed and compared toexpected results. A total of 8 of the 48 targets were ligated to a poolof 3840 labels (counters). The assay was as shown in FIG. 3. Theconditions were single strand deoxyoligonucleotide ligation using aphage RNA ligase to join the labels with targets. Universal primingsites on the targets and labels were included to enable PCRamplification of the joined label-targets. The ligation conditions wereessentially as described in (Tessier, D. C. et al. (1986) Anal Biochem.158, 171-178, 50mM Tris-HCl, pH 8, 10 mM MgCl2; 10 ug/mL BSA, 25% PEG, 1mM HCC, 20 uM ATP; 5:1 acceptor (labels) to donor (the 8 targets) ratioat 25 C overnight. The products were amplified using PCR, purified,biotin labeled with TdT, hybridized to the array, washed, stained, andscanned. The expected 8 blocks show hybridization to the array in theexpected patterns.

Different ligation conditions were also tested by ligating either asingle target or a pool of 48 targets to the 3,840 counters. Theconcentrations of the targets used in the experiment were high as in theprevious experiment so most counters will be ligated to targets. Inligation 1 a single target was ligated to 3,840 labels. In ligation 2,48 targets at 1:1 copy number were ligated to 3,840 labels. Ligation 3is a negative control for PCR so no DNA was added. PCR with the pair ofuniversal primers was performed using the ligation products as templateand the products separated on a gel. As expected a band was observedfrom ligations 1 and 2, but not 3. The PCR products were labeled andhybridized to the array and the scan images after array hybridizationwere analyzed. As expected no signal was observed for ligation 3, all ofthe targets were observed for ligation 2 and the single expected targetwas observed for ligation 1.The single target lights up in the correctregion of the chip, but background signal was also observed inunexpected locations. Increased stringency of hybridization conditionscan be used to minimize hybridization to unexpected probes of the array.

In another example, conditions for optimization of hybridization todecrease cross hybridization were tested. The products used were asdescribed above and hybridization was performed with formamide and withor without non-specific competitor (herring sperm DNA). The non-specificsignal is significantly decreased in the presence of formamide, with andwithout non specific competitor. This demonstrates that even though thetargets and counters alone have 15 bases of complementarity to probes onthe array, the combination of target plus counter and the resultingincrease to 30 bases of complementarity to the probes, results inspecific hybridization. Within the block of 3,480 probes, there isheterogeneity in the hybridization intensity. Preliminary sequenceanalysis shows a strong correlation of GC content with high signals. Tominimize this array probes may be selected to have similar melting tempsfor the counters or the target-counter combination may be optimized toobtain similar hybridization stabilities. For example, if two targetsare to be analyzed the portions of each target that are to be part ofthe probe may be selected to have similar TMs.

To test the efficiency of T4 RNA ligase in the ligation of labels totargets, DNA ligase from E. coli was tested. This required a slightmodification of the sample prep (as depicted in FIG. 7) by creating anoverhang site for duplex ligation. The target in this example has adouble stranded target specific portion and a single stranded overhang.The overhang may be, for example, a run of inosine bases, for example 6to 9, or a string of random bases, for example, N6-16. DNA ligase isused to close the gap and generate a ligated product that includes thetarget strand and a label/counter from the pool of 3,840 counters. ThePCR is carried out in the same manner as above using common primers.

The expected targets were observed, but some non-specific bands werealso detected in the amplified DNA, even in the absence of the target.This suggests that the some of the 3,840 labels are combining with eachother when this method is used. Selection of an optimized pool of labelsmay be used to mitigate such interference.

In another example random primed PCR was tested. Instead of a ligationstep, the targets have a 3′ random region, that can be, for example, adegenerate region or an inosine region. The labels hybridize to therandom region and the random region is used as a primer for extensionthrough the label during the PCR step to append a copy of the label andthe universal priming site at the 5′ end of the label oligo to the 3′end of the target. The extended target has a copy of the label sequenceand the universal priming sequence and can be amplified by PCR.

In another example, a purification method for removing excess un-ligatedcounters was tested. The method is shown schematically in FIG. 11. Thecounters 101 and the targets 2103 are ligated to form counter-targetmolecules as shown previously. A support bound probe that iscomplementary to the universal primer at the end of the targetoligonucleotides 2105, is used to separate counter-targets and targetsfrom un-ligated counters. The support 2109 may be, for example, amagnetic bead. A second separation can be used to separatecounter-targets from un-ligated targets. The second separation uses asupport bound probe complementary to the universal priming sequence atthe end of the counters 2107. The single capture reduces backgroundamplification. A double round of capture may also be used.

In FIG. 18 a scatter plot is shown to illustrate one way of representingthe combinations of different target occurrences ligated randomly todifferent labels in the set. The plot shows combinations for 20different target occurrences (labeled 1 to 20) representing 20 copies ofthe same target. The Y-axis represents different labels identified by anumber from 1 to 1000. Each of the targets can be labeled with any ofthe 1000 labels, for example target 1 is labeled with label 351 and hascoordinates (1, 351). The labels are distinct and distinguishable whilethe targets are the same in this example.

FIG. 19 shows a schematic where genomic DNA 1901 is fragmented, forexample at restriction sites 1903 to produce fragments 1905. Thefragments are ligated with labels to form fragments labeled at both ends1907. All fragments can be ligated to the labels The label-ligatedfragments are circularized, for example, by ligation of the label endsto form closed circles 1909 with first and second labels forming asingle label 1911. The circularized fragments can be treated withexonuclease to remove unligated fragments. The circle and label can beamplified using gene-specific PCR primers 1913. The PCR product has thelabel region 1911 flanked by target specific regions. The array probe ispreferably complementary to the junction between the target specificregion and the label. There are two such junctions 1915 and 1917 in thePCR product and each could be targeted on either strand (since theproduct is double stranded). The products may be fragmented, labeled andhybridized to an array of probes to the junctions. The label-targetcombination can be hybridized to an array for counting.

FIG. 20 shows a graph of counting efficiency on Y axis and copies oftarget on X axis. The different lines represent different numbers oflabels being used, from 1000 to 10,000. The inset graph is a blow up ofthe upper left hand region of the larger graph and shows how countingefficiency changes with the number of labels. Fewer labels results in amore rapid decrease in counting efficiency as the number of targetsincreases.

FIG. 21 is a plot of labels observed per target as the copies of targetsincreases and the number of label types increases.

In another embodiment, illustrated schematically in FIG. 5, genomic DNA1901 is fragmented with a restriction enzyme, for example, BamHI, whichgenerates a single stranded overhang for sticky ended ligation. Thefragments 1905 are ligated to adaptors 2207 that include a label 2205and a universal priming site 2203. Different adaptors vary in the labelportion 2205 but have a common priming site 2203. The label is 3′ of theuniversal priming site so that it is between the fragment and theuniversal priming site. The adaptor ligated fragments are amplified byPCR using primer 2209. The PCR product can be fragmented, labeled with adetectable label and hybridized to an array. The resulting strands aredetected by hybridization to an array having target-label probes 2210and includes different features for each target-label combination. Thearray has a different feature for each target-label-tag combination. ThePCR amplicons may be fragmented prior to array hybridization. Preferablythe fragments are labeled, for example, by TdT incorporation of anucleotide that can be detected, such as a biotin containing nucleotide.

The probes of the array are complementary to the junction between thelabel and the restriction fragment. The sequences at the ends of theindividual strands of the restriction fragments are predicted based onin silico digestion of the human genome. Also, fragments are targetedthat are within the size range that is known to amplify efficiently byadaptor ligation PCR, for example, 200 bases to 2 kb. The adaptor 2201had two segments, a constant priming region 2203 and a variable labelregion 2205. Together 2203 and 2205 form the label adaptor 2207. Theprimer 2209 has the same sequence 5′ to 3′ as the 2203. The schematic isdrawn showing only one strand, but one of skill in the art wouldunderstand that in a preferred embodiment the genomic DNA is doublestranded and the restriction fragments have two strands, which may bereferred to as a top strand and a bottom strand. The convention is thatthe top strand is drawn 5′ to 3′ left to right and the bottom strand isthe complement of the top strand and is drawn 3′ to 5′ left to right.Adaptors are preferably double stranded for at least a portion of theadaptor, they may have single stranded overhangs, for example to have“sticky ends” that facilitate hybridization and ligation to the overhangresulting from restriction digestion. In a preferred aspect, the sameadaptor can be ligated to the two ends of a strand of a restrictionfragment and may be ligated to one or both strands. The adaptor may beligated to the ends of the top strand in opposite orientations as shownin FIG. 22, so that the label is internal to the priming site at bothends. The adaptor may have a top and a bottom strand and the top strandmay be ligated to the top strand of the fragment and the bottom strandligated to the bottom strand of the fragment. The top and bottom strandsof the adaptor may be complementary over the entire length, but oftenhave single stranded regions at one end to facilitate sticky endedligation to an overhang created by a restriction enzyme.

To test this method several adaptors were generated. The test adaptorhas PCR002 (SEQ ID No. 1969) as top or sense strand and BamAdaAS (SEQ IDNo. 1970) as bottom or antisense strand.

PCR002 5′ ATTATGAGCACGACAGACGCCTGATCT (1969) BamAdaAS 3′AATACTCGTGCTGTCTGCGGACTAGACTAG 5′P (1970)The single stranded region on the right is the BamHI single strandedoverhang. Te adaptor also has a half Bgl II site. The “fulllength-label” adaptor has SEQ ID No. 1972 as top or sense strand and SEQID No. 1973 as bottom or antisense strand.

Sense 5′ ATTATGAGCACGACAGACGCCTGATCTNNNNNNNNNNNNNNT AntiSense 3′AATACTCGTGCTGTCTGCGGACTAGANNNNNNNNNNNNNNACTAGA 5′ phosphate may be added to one or both strands of the adaptor using,for example, T4 polynucleotide kinase. In some aspects a truncatedadaptor may be used. An example of such an adaptor is shown in FIG. 7,the top or sense strand is SEQ ID No. 1974 and the bottom or antisensestrand is SEQ ID No. 1975. The portion of the sequence that has a linethrough it for both SEQ ID NOs. 1974 and 1975 indicates bases missing ascompared to SEQ ID NOs. 1972 and 1973 respectively. The N′s in SEQ IDNos. 1972-1975 indicate a variable sequence in the adaptor that isdifferent for each different label. For example, if there are 1,920different labels to be used then the N₁₄ represents the 1,920 differentlabels.

In some aspects it is preferable to use shorter oligos. The full lengthadaptor in includes 87 bases. The truncated adaptor has 57 bases. Since2 different oligos must be synthesized for each different label adaptor(e.g. 1,920 labels requires 3,840 different oligos) shorter adaptors aremore economical. The separate oligos are preferably annealed togetherprior to being combined into a pool for ligation to fragments. Theprimer may be, for example, SEQ ID NO. 1969 or the 5′ 17 bases of SEQ IDNo. 1974.

FIG. 24 shows the results of a control experiment where the test adaptorwas ligated to fragmented genomic DNA and analyzed on an array havinggenomic probes. The DNA was subjected to fragmentation with a BamHI, thetest adaptor was ligated to the ends and SEQ ID No. 1969 was used as aprimer for PCR amplification. The PCR products were fragmented and endlabeled using TdT and hybridized to a CNVtype and HG49 arrays. The upperplot is the number of probes (number of different features where eachfeature corresponds to a different probe sequence) complementary torestriction fragments in the different size bins shown on the X-axis.The sizes and sequences of restriction fragments from a selected genomecan be predicted and binned according to size. The probes of the tilingarray (probes essentially all non-redundant sequences in the genome) canbe assigned to the restriction fragment to which the probe iscomplementary. Longer fragments will have larger numbers of probes thatare complementary to that fragment, simply because the fragment islonger. Restriction fragment size is distributed based on the frequencyof the occurrence of the recognition site. Note that the X axis does notincrease linearly. While there are more probes that are complementary tofragments in the bins of size greater than 3000, particularly in thebins between 9000 and 30,000, but the intensity in those size bins isless than the intensity of the bins that are about 400 to about 1800.The larger fragments, greater than 9000 bases, for example, do notamplify efficiently with PCR, resulting in lower representation of thoselarge fragments in the hybridization.

In another example, a truncated label adaptor was used (SEQ ID Nos. 1974and 1975). The adaptor ligated fragments were extended to fill in theends with polymerase prior to PCR. Hybridization was done in duplicateto either the CNV-type array or HG49 design C. Fragmented DNA andnon-fragmented DNA were plotted. The intensity of the DNA that was notfragmented prior to hybridization is less than the intensity of thefragmented DNA. The peak of the intensity for both plots is at afragment size of about 900 base pairs.

FIG. 11 shows a theoretical modeling of the number of counters predictedto be observed at least once 3201, exactly once 3202 or exactly twice3203.l A non-depleting reservoir of 960 diverse labels was considered.Equation (1) was used to calculate the at least once curve, equation (2)the exactly once curve and equation (3) the exactly twice curve. Theerror bars indicate one standard deviation from the corresponding meanvalue.

$\begin{matrix}{{E\lbrack k\rbrack} = {m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}} & (1) \\{{{Var}\lbrack k\rbrack} = {{{m\lbrack {1 - ( {1 - \frac{1}{m}} )^{n}} \rbrack}( {1 - \frac{1}{m}} )^{n}} + {{m( {m - 1} )}\lbrack {( {1 - \frac{2}{m}} )^{n} - ( {1 - \frac{1}{m}} )^{2n}} \rbrack}}} & (2)\end{matrix}$

FIG. 12 shows counting results for DNA copy number titrations usingmicroarray hybridization in (A) or DNA sequencing in (B). Dilutions(3.62 ng, 1.45 ng, 0.36 ng and 0.036 ng) of a DNA sample isolated fromcultured lymphoblasts of a Trisomy 21 male individual were processed formicroarray hybridization (left) and DNA sequencing (right). Threechromosome targets were tested and observed numbers of counters (Y-axis)are shown (curve 1201). The number of target molecules for each sample(X-axis) was determined from the amount of DNA used, assuming a singlecell corresponds to 10 pg. For comparison, the theoretical counter usagerates from the stochastic model equation are also plotted 1202.Numerical values are provided in Table 4.

BamHI cuts the human genome into an estimated 360,679 fragments with asize distribution of 6 bp to 30,020,000 bp. The median size is 5142 bpand the mean is 8320 bp. There are 79,517 fragments in the size range of150 bp to 2 kb. For testing it may be desirable to choose fragments thatmeet selected criteria, for example, within a selected size range,select fragments that have more than 1 probe on the HG49m array, excludefragments that are in known CNV regions, or exclude fragments having aSNP in the first or last 20-30 bases.

The upper panel of FIG. 26 shows the intensities of 1,152 array probesassociated with one gene target on chromosome 4, chr4_01s. The data arefrom the array with 5 ng DNA, i.e., 1000 copies of the tested genetarget. The 1,152 probes shown share the same genomic sequence portion,but have different label sequences. Each black dot represents one labelsequence. The left 960 dots (on the left side of the red vertical line)correspond to specific labels (i.e., labels used in ligation reaction),and the right 192 dots correspond to non-specific labels (i.e., labelsnot used in ligation reaction). The probe intensities were plotted innatural log scale on the y-axis. The blue horizontal line is thethreshold determined by analysis algorithm (see Materials and Methods),which has a value of 3,800.

The array design for the experiment represented in FIG. 26 is asfollows. For each gene target assayed, the array probe consists of allpossible combinations of the 960 label sequence and either of the twoBamHI genomic fragment ends. An additional 192 label sequences that werenot included in the adaptor pool were also tiled to serve asnon-specific controls. This tiling strategy enables consistency check onthe number of labels used at the paired ends, since each target fragmentis ligated to two independent labels (one on either end), and for thesame target fragment, the counts on the left and right side should bevery similar.

The lower panel shows the histogram of the intensity data correspondingto 960 specific labels. Also shown in the figure are the 2 fitted normaldistributions, designated by red and green curves, respectively. Thefitted distributions have the mean and standard deviation of 1447±680and 12186±3580, respectively. The blue vertical line is the threshold,which has the same value as the blue horizontal line shown in the upperpanel. Based on such threshold, 501 probes (i.e., labels) were countedas “used”.

FIG. 27 shows the number of times observed for each of the 960 specificlabels. Empirically, we did not observe 349 labels in any of the 20cases. By model, we would expect to observe 643.05±9.96 labels at leastonce, which means we expect not to observe 307˜327 labels. This resultshown was obtained by grouping labels used in independent ligationreactions together. To more accurately estimate the frequency of usageof labels, only data from experiments with low concentrations (0.05 ngand 0.5 ng of DNA ligation amount) were considered. Under eachconcentration, 5 different gene targets independently ligated to labelsat both ends. Therefore, a total of 20 independent reactions (2concentrations×5 gene targets×2 ends) were grouped together. Of thesereactions, 1,064 labels were observed; some were observed more oftenthan the others, the frequency of usage of labels ranges from 0 to 6.

FIG. 28 shows one example of the replication process of 500 copies of agene target. In each subplot, copies of target molecules were plotted inthe same order. The y-axis is the relative ratio of the number ofamplified molecules over the minimal number of amplified molecules ineach PCR cycle. Before PCR, all copies are of equal amount, i.e., eachcopy has one molecule at cycle 0 (subplot (a)). As the PCR process goeson, we start to see differences in the number of amplified moleculescorresponding to different copies of target molecules. For example, incycle 3 (subplot (b)), the ratio between most and least abundant ofamplified molecules is 4. Such ratio becomes larger as the number of PCRcycle increases. In cycle 8 and 15, the ratio becomes 26 and 30, incycles 8 and 15 respectively (see subplots (c) and (d)). This suggeststhat the differential usage of labels may be observed before PCR isstarted. Such difference in the amount of molecules associated withdifferent labels will carry on as PCR process goes on.

PCR simulation. We defined n copies of a gene fragment T, each ligatedto a single counter randomly selected from an infinite pool of m uniquecounters to generate a collection of k resulting counter-ligated genetarget molecules T*={tl_(i), i=1,2, . . . , k}. We assumed that eachcounter-ligated gene target molecule tl_(i) replicates randomly andindependently of other target molecules; and that the replicationprobability p (i.e., amplification efficiency) of different molecules,tl_(i), remains constant throughout the PCR process. For each tl_(i), wedenote the number of molecules at PCR cycle c as N_(i) ^(c). When c=0,N_(i) ⁰ is the initial number of tl_(i). The PCR process at cycle c+1can be modeled as a series of N_(i) ^(c) independent trials thatdetermine the replicability of each of the N_(i) ^(c) molecules withreplication probability p. Let ΔN_(i) ^(c) represent the number ofmolecules replicated at cycle c+1, then the number of molecule tl_(i)after cycle c+1 is N_(i) ^(c+l)=N_(i) ^(c)+ΔN_(i) ^(c), where theprobability of ΔN_(i) ^(c) is

$\begin{matrix}{{p( {\Delta\; N_{i}^{c}} \middle| N_{i}^{c} )} = {\begin{pmatrix}N_{i}^{c} \\{\Delta\; N_{i}^{c}}\end{pmatrix}{{p^{\Delta\; N_{i}^{c}}( {1 - p} )}^{N_{i}^{c} - {\Delta\; N_{i}^{c}}}.}}} & (2)\end{matrix}$We determined the relative abundance of different counter-ligated genetarget molecules tl_(i) upon completion of the simulated PCR run forn=500, 50, or 5, and p=0.8, 0.7 or 0.6 (Table 5). In each case, weperformed 1,000 independent runs to simulate 30 cycles of adaptor PCR,followed by 30 cycles of gene-specific PCR.

Table 5. Shows summary statistics drawn from 100 independent simulationruns modeling PCR, ligation at each end of targets is considered.

Initial copy number N = 5 N = 50 N = 500 Side Left Right Left Right LeftRight # of labels 5 5 48.61 0.99 48.64 1.09 388.91 389.27 observed 6.857.18 Max (1.43 0.19) * (1.43 0.19) * (2.18 0.49) * (2.13 0.47) * (4.520.59) * (4.44 0.55) * 10{circumflex over ( )}11 10{circumflex over( )}11 10{circumflex over ( )}10 10{circumflex over ( )}10 10{circumflexover ( )}9 10{circumflex over ( )}9 Min (5.73 2.27) * (5.73 2.27) *(2.35 1.06) * (2.35 1.06) * (1.15 0.49) * (1.23 0.49) * 10{circumflexover ( )}10 10{circumflex over ( )}10 10{circumflex over ( )}910{circumflex over ( )}9 10{circumflex over ( )}8 10{circumflex over( )}8 Ratio btw 3.13 2.44 3.13 2.44 14.10 13.87 43.42 44.92 max & min11.41 13.42 25.66 30.04 Mean (1.00 0.16) * (1.00 0.16) * (1.03 0.06) *(1.03 0.06) * (1.27 0.03) * (1.27 0.03) * 10{circumflex over ( )}1110{circumflex over ( )}11 10{circumflex over ( )}10 10{circumflex over( )}10 10{circumflex over ( )}9 10{circumflex over ( )}9 Standard (3.441.02) * (3.44 1.02) * (3.98 0.52) * (3.94 0.54) * (6.75 0.41) * (6.690.40) * deviation 10{circumflex over ( )}10 10{circumflex over ( )}1010{circumflex over ( )}9 10{circumflex over ( )}9 10{circumflex over( )}8 10{circumflex over ( )}8 Coef. of 0.36 0.13 0.36 0.13 0.39 0.050.38 0.05 0.53 0.03 0.53 0.03 variation

Focusing on the experiments with concentrations of 0.5 and 0,05 ng,(3^(rd) and 4^(th) in each group of 5), which provide the most accuratecount of labels, there are 20 different opportunities for a given labelto be observed (2 concentrations×5 amplicons×2 sides (left or right)).We observed 1,064 labels over the 20 opportunities.

To observe the distortion of the relative abundance of DNA molecules inthe reaction resulting from the PCR process, dispersion in thequantitative distribution of PCR amplified DNA molecules was analyzed. Amodel of the PCR process was generated to understand the dispersion inthe distribution of amplified molecules (FIG. 25, Table 6). A series of1,000 independent simulation runs were performed to simulate thereplication of uniquely labeled target molecules through PCR processes.For each run, we measured the distribution of the final amount of PCRproducts and quantified the dispersion of distribution using twomeasures: ratio of the maximal to the minimal amount, and coefficient ofvariation of final PCR products. This demonstrates that the degree ofdispersion increases with the incidence of replicate use of identicalcounters, which may be in-part responsible for the deviation observedwhen assaying high target copy numbers. Table 6 lists the ratio and CVfor distributions corresponding to different concentrations andreplication probabilities (one sided ligation considered).

TABLE 6 replication probability n = 5 n = 50 n = 500 Ratio of max to minp = 0.6 5.69 ± 4.95 26.16 ± 23.78 124.18 ± 88.04  amount of PCR p = 0.74.59 ± 8.03 16.22 ± 15.53 71.55 ± 55.13 amplified product p = 0.8 2.82 ±1.51 11.54 ± 9.53  42.24 ± 27.49 Coefficient of p = 0.6 0.48 ± 0.16 0.51± 0.06 0.62 ± 0.03 Variation (CV) p = 0.7 0.41 ± 0.14 0.44 ± 0.05 0.57 ±0.02 p = 0.8 0.34 ± 0.12 0.36 ± 0.05 0.52 ± 0.02

Example 1 of a method for selecting a collection of labels starting withall possible 14 mers (4¹⁴ or ˜268 million possible labels). Step 1:clustering based on the last 7 bases: all sequences with the same last 7bases are grouped together; within each cluster, randomly pick onesequence, this gives us 11,025 sequences, denoted by set A. Step 2:clustering based on the first 7 bases: all sequences with the same first7 bases are grouped together; within each cluster, randomly pick onesequence, this gives us 13,377 sequences, denoted by set B. Step 3: getthe union set of set A and B, the combined set has 24,073 sequences.Then do clustering based on the middle 6 bases, randomly pick onesequence out of every cluster, this gives us 3,084 sequences, denoted byset C. Step 4: calculate the all-against-all alignment score of set C,which gives us a 3,084×3,084 self-similarity score matrix, denoted by S.Step 5: filter based on the score matrix. If an element of the scorematrix S(i,j) has a high value, that means, the corresponding sequencesi and j are very similar to each other. Starting from the elements withtop self-similarity score, randomly pick one and discard the other;repeat this process until the number of retained sequences <2000. Untilthis step, 1,927 sequences were retained.

For the retained 1,927 sequences, an all-against-all complement scorewas calculated for each. This gave a 1,927×1,927 cross complement scorematrix. A step similar to step 5 was performed, to avoid labels withmaximal cross-complement with other labels. Starting from the pairs withtop cross-complement score, one was randomly pick and the otherdiscarded. This process was repeated until the number of retainedsequences was 1920. Next the 1920 labels were split into 2 sets, withone set (denoted by set A) consisting of sequences that are maximumdifferent from one-another; and the other set (denoted by set B)consisting of the remaining sequences. The procedure used to splitsequences was as follows. Starting from the original 1920 by 1920similarity score matrix, for each sequence, (1) sum up all itssimilarity scores with the rest of the sequences in the pool, that is,for each sequence, calculate a total similarity score. (2) Sort thetotal similarity scores of all sequences and select the sequence withthe lowest total score, and move it to set A. (3) Remove the row andcolumn corresponding to the selected sequence, i.e., both the number ofrows and columns in the similarity score matrix are reduced by 1. Repeatsteps 1-3, until the number of rows and columns in the similarity scorematrix reaches 960 or half of the original. The selected sequencesbelong to set A and the remaining sequences belong to set B.

In another embodiment a collection of labels is selected using thefollowing steps. Starting with all possible 14 mers (4¹⁴ or ˜268 millionpossible labels) eliminate all that do not have 50% GC content.Eliminate those were each nucleotide does not occur at least twice.Eliminate those that have more than two G/C in tandem or more than threeA/T in tandem. Eliminate those that contain a selected restriction site.That reduces the original set to ˜33 million or 12.43% of the originalset. From that set select those that have a Tm within the range of 38.5°C. to 39.5° C. This step results in a set of ˜7 million or 2.73% of theoriginal set. Remove those that have regions of self-complementarity.

The resulting set in this example was now 521,291. A hierarchicalclustering was performed to identify a set that has maximum sequencedifference between one-another. The resulting set contained 1,927labels. Labels were removed if the sequence had a tendency to bind toother labels in the set. This reduced the set to 1,920 labels. A finalset of 960 labels was selected from the 1,920 as being maximallydifferent for the “specific” labels and 192 additional counters to tileon the array as “non-specific” controls.

Selection of Targets and design of test array. Regions selected to assayas targets included Chr X, Chr Y, Chr 4 as a reference and Chr 21 forTrisomy. Locations on the chromosomes for assaying were selected toavoid centromeres and telomeres. Fragments were selected based on Bam HIfragments of between about 400 and 600 base pairs. Fragment intensitywas checked using HG49 array hybridization. The first and the last 26nucleotides of the fragments (from and including the Bam HI site) weretiled. Repeats were avoided and GC % was optimized.

The array format was 100/25. Feature size is Sum. There are 436×436features or 190,096 features. Synthesis was NNPOC, 43 mer probes, 5′ up,no phosphate. The chip name is STCL-test2. The gridding probe used wasthe same as the HG49. No QC probes were included.

Aside from reducing whole chromosomes into 360,679 smaller molecularweight DNA pieces more suitable for ligation reactions, restrictiondigestion also serves to reduce the overall sequence complexity of thesample, as only an estimated 79,517 fragments reside in the 150bp-2kbsize range that is effectively amplified by PCR. To detect and quantifycounters that have been selected by the target molecules, the labeledgenomic target fragments may be circularized and PCR amplified toprepare for analysis, for example, using microarray hybridization or DNAsequencing. A representative BamHI target fragment was sampled for eachof the three test chromosomes. Simultaneous measurements of all threechromosomes serve as an internal control independent of dilution orother systematic errors. A suitable DNA array detector capable ofdistinguishing the set of counters bound to copies of the targetmolecules was constructed using photolithography (S. P. Fodor et al.,Science 251, 767 (Feb. 15, 1991).). Each array element for a target tobe evaluated consists of a target complementary sequence adjacent to oneof the complements to the 960 counter sequences (FIGS. 1 and 2A). Forincreased specificity, a ligation-readout was performed on themicroarray after hybridization to avoid false positive detection of thecross-hybridization of identical targets with different counters. As ameans of validation through a secondary measure, samples hybridized tomicroarrays were subsequently sampled by DNA sequencing (FIGS. 10 and29).

An equation to model the stochastic labeling of target molecules with asmall library of 960 counters, and validate our equation model withnumerical simulations is disclosed. In the model, the diversity ofcounters selected by, and ligated to target molecules in the reactionsolution (simplified as ‘used’) is dictated by the number of copies ofmolecules present for each target fragment in the reaction (FIG. 12).Under conditions where the size of the counter library is much greaterthan the number of copies of a given target molecule, the countingefficiency is high, and counting the number of counters used isequivalent to counting the number of copies of the original targetmolecules (FIG. 16). When the number of target copies approaches andexceeds the number of different counters in the reaction, any counter inthe library is more likely to be used multiple times (FIG. 15). Thenumber of counters used at least once is an important measure because itserves as the basis for drawing yes/no conclusions in our digitalreadout on microarrays. Under stochastic labeling conditions, we expectthat the absolute quantity of single DNA molecules can be accuratelydetermined by proxy counts of labeling events. Indeed, microarrayexperiments demonstrate a high degree of correlation between the numberof copies of target molecules added to the reaction and the number ofcounters used, as detected on microarrays (FIG. 12). In particular,counter usage precisely profiles the number of target molecules underconditions of high counting efficiency. Subtle deviations from the modelmay represent minor dilution errors in the preparation of the sample.However, within that sample dilution, the relative counter ratios of thethree internally built-in markers are highly accurate (FIG. 13). FIG. 13shows comparison of relative copy ratios of the three gene targetstested: ChrX, Chr4 and Chr21 representing genetic material of one, twoand three copies per cell. Different dilutions (5 ng, 2 ng, 0.5 ng and0.05 ng) of a DNA sample isolated from cultured lymphoblasts of aTrisomy 21 male individual were processed for microarray hybridizationand DNA sequencing. The calculated number of target molecules (see,Table 4, column 9) was inferred from the number of counters detected onmicroarrays (A), and was also calculated for the SOLID sequencing data(B). For each sample dilution, the target copy number ratio of each genetarget relative to ChrX is shown.

On the other hand, when target copies exceed ˜100, detected labelingevents appear to indicate fewer than actual molecules in solution (FIG.12 inset in graph on left). This deviation was reproducible andconsistently observed across multiple microarray experiments, and wasalso observed in the DNA sequencing experiments (FIG. 12 inset in graphon right). Under-counts of expected labeling events may originate frominadequate detection sensitivity of the microarray platform or fromother systematic or indeterminate deficiencies in the sample preparationprocedure. PCR, for example, is prone to amplification bias (T.Kanagawa, J Biosci Bioeng 96, 317 (2003) and M. F. Polz, C. M.Cavanaugh, Appl Environ Microbiol 64, 3724 (1998)), which could hinderthe comprehensive detection of labeling events that may be genuinelystochastic.

To confirm the microarray results, a digital sequence counting ofindividual molecules in the DNA samples hybridized to microarrays wasused as a means of validation, and to detect the presence of any falsenegatives that may have escaped microarray detection. Analysis of mappedsequence reads resulted in counts in agreement to the microarrayobservations. Furthermore, a second, independent sequencing run wasrepeated with similar findings (Table 3).

An additional feature of digital sequence counting is that unlike themicroarray intensity data (FIGS. 22 and 23), which offers lowerresolution into the measurement of the concentration dispersion of PCRamplified molecules, sequence counting clearly demonstrates significantvariation in the representation of amplified targets (FIG. 29), This isconsistent with the computed PCR model. Overall, detected counters onthe microarray and sequencing experiments correlate well, but a smallsubset of counters appear to be unique to each process (Table 7). Theobserved number of labels in common between the microarray and the twosets of sequencing experiments are summarized in the table. The numberof labels in each category is included. The categories are as follows:A+1+2 for labels detected in each of the 3 experiments, 1+2 for labelsdetected only in sequencing runs 1 and 2, 1+A for labels detected insequencing run 1 and by array, and so on for the amounts of DNA shown incolumn 3.

TABLE 7 A + 1 + 1 + 1 + DNA sample 2 2 A 2 + A 1 2 A Chr4 Left side0.036 ng  13 0 0 0 0 0 1 0.36 ng 96 3 0 1 2 2 5 1.45 ng 228 13 4 22 6 106 3.62 ng 484 23 2 3 4 6 12 Right side 0.036 ng  14 0 0 0 0 0 0 0.36 ng100 1 0 0 2 2 7 1.45 ng 249 25 2 0 15 33 5 3.62 ng 511 22 2 1 9 23 11Chr21 Left side 0.036 ng  18 0 2 0 0 0 0 0.36 ng 150 0 2 4 0 7 4 1.45 ng324 17 8 1 32 16 2 3.62 ng 637 14 10 0 17 14 4 Right side 0.05 ng 18 0 11 0 0 0 0.36 ng 144 0 2 2 0 0 9 1.45 ng 330 34 2 3 15 12 6 3.62 ng 61529 1 7 5 2 4 ChrX Left side 0.036 ng  11 0 0 0 0 0 0 0.36 ng 42 0 0 0 13 8 1.45 ng 137 3 1 5 8 5 5 3.62 ng 274 12 0 2 4 12 5 Right side 0.036ng  10 1 0 0 1 0 0 0.36 ng 43 0 3 0 4 0 2 1.45 ng 127 15 0 0 11 25 63.62 ng 298 12 3 3 24 31 2

For the reverse scenario, high numbers of mapped sequence reads werealways observed to correlate with high microarray intensities in theseexamples. No systematic or sequence correlations, or explanations wereidentified for the counters that are absent from any given sequencingexperiment for which the microarray readout demonstrates a strongsignal. While obviously underrepresented in some experiments, the samecounters are sometimes present in high sequence counts in otherexperiments, suggesting that they are available for sequencing. PCR wasused to resolve these isolated cases of disagreement and demonstratethese were false negatives in the sequencing experiments (Table 3).Despite their presence in the sequencing library, it is unclear why thecounters were not observed or were underrepresented in the originalsequencing run, and also in the subsequent replicate sequencing run.

Aside from the comparative analysis of absolute and relative counts ofthe numbers of target molecules and counter labels, additional ways toassess the stochasticity of the labeling process were evaluated. First,if the labeling process is random, the frequency of incorporation ofidentical counters in independent events across the paired left andright termini of target fragments should closely resemble outcomes fromnumerical simulation. Observed counts on microarrays do in fact matchclosely with numbers obtained from computer simulations (Table 4,columns 10-11). Second, if the target molecules are labeled randomlywith an equal likelihood of incorporation for any member of the 960counters in the library, we would expect the number of repeatedobservations of counters to follow a stochastic nature. For thisanalysis, we accumulated a total of 1,064 counter observations overseveral microarray experiments restricted to low target copy numbers.Exclusion of data from high copy targets was necessary to avoidundercounting labeling events from multiple incidences of identicalcounters attaching individually to numerous target copies. As a furtherand final demonstration of stochastic labeling, results show that thefrequency of label usage follows a pattern consistent with outcomes fromnumerical simulation.

CONCLUSION

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby. All cited references, including patent and non-patentliterature, are incorporated herein by reference in their entireties forall purposes and particularly to disclose and describe the methods ormaterials in connection with which the publications are cited.

That which is claimed is:
 1. A method for determining a number ofoccurrences of a target molecule from a single cell, the methodcomprising: a) generating an indexed library by performing a labelingstep, the labeling step comprising: i) combining each of a targetmolecule from a plurality of target molecules from a single cell with alabel-tag from a plurality of diverse label-tags, wherein the ratio ofthe number of the plurality of diverse label-tags to the number of eachof the plurality of target molecules is greater than 5; and ii)generating the indexed library comprising a plurality oftarget-label-tag molecules by hybridizing the label-tag of the pluralityof diverse label-tags to the target molecule of the plurality of targetmolecules and performing an extension reaction, wherein atarget-label-tag molecule comprises the label-tag and a portion of acomplementary sequence of the target molecule; b) amplifying theplurality of target-label-tag molecules from the indexed library togenerate a plurality of amplified products; and c) sequencing at least aportion of the plurality of amplified products of step (b) to determinea number of different label-tag sequences associated with the portion ofthe complementary sequence of the target molecule from the single cell,wherein the number of different label-tag sequences indicates the numberof occurrences of the target molecule from the single cell.
 2. Themethod of claim 1, wherein the sequencing of step c) results indetection of the portion of the complementary sequence of the targetmolecule.
 3. The method of claim 1, wherein the method is multiplexed.4. The method of claim 1, wherein the plurality of target moleculescomprise nucleic acid molecules.
 5. The method of claim 4, wherein thenucleic acid molecules comprise genomic DNA.
 6. The method of claim 4,wherein the nucleic acid molecules comprise cDNA.
 7. The method of claim4, wherein the nucleic acid molecules comprise RNA.
 8. The method ofclaim 7, wherein the RNA is mRNA.
 9. The method of claim 1, wherein thetarget molecule from the single cell comprises a polymorphism.
 10. Themethod of claim 9, wherein the polymorphism is a single nucleotidepolymorphism.
 11. The method of claim 9, wherein the polymorphism is anindel.
 12. The method of claim 1, wherein the combining is conducted ina specified container.
 13. The method of claim 12, wherein the specifiedcontainer comprises a well.
 14. The method of claim 1, wherein theplurality of label-tags are attached to a bead.
 15. The method of claim1, wherein a label-tag of the plurality of label-tags further comprisesat least one universal primer.
 16. The method of claim 1, wherein eachlabel-tag of the plurality of label-tags further comprises a commonsequence.
 17. The method of claim 1, wherein a label-tag of theplurality of label-tags further comprises a target-specific recognitionsequence.
 18. The method of claim 1, wherein a label-tag of theplurality of label-tags further comprises an oligo dT sequence.
 19. Themethod of claim 1, wherein the plurality of label-tags comprises two ormore target-specific recognition sequences.
 20. The method of claim 1,wherein the plurality of label-tags comprises between 100 and 10,000different label-tag sequences.
 21. The method of claim 1, wherein theamplifying comprises performing a polymerase chain reaction.
 22. Themethod of claim 1, further comprising storing the indexed library. 23.The method of claim 1, further comprising performing the steps ofamplifying and sequencing multiple times.
 24. The method of claim 1,wherein the hybridization of the label-tags to target molecules isstochastic.
 25. The method of claim 1, wherein the sequencing stepcomprises determining a genotype.
 26. The method of claim 3, wherein thesequencing step comprises determining a gene expression profile.
 27. Themethod of claim 1, wherein the single cell is a human cell.
 28. Themethod of claim 1, wherein the single cell is a tumor cell.
 29. Themethod of claim 1, wherein the single cell is a bacterium.
 30. Themethod of claim 1, wherein the hybridization of the label-tags to targetmolecules is performed under a stringent condition.